./. genotype despite DP coverage equal to number of reads in reference AD field

I came across some unusual variants called by HaplotypeCaller running in gvcf mode while working on human WGS data (the example gvcf line can be seen below).
The genotype in almost all samples is undefined i.e. "./.", despite the good coverage reported in DP field (only one sample is identified as 0/1). Moreover, in "./." genotyped samples all reads fall into reference allele group of AD field, therefore I would anticipate "0/0" genotype rather than "./.".
I have also inspected several bam files visually and did not find any obvious mapping problems. I have attached two IGV snapshots of the variant region: first is from an example "./." genotyped patient and second one is from the only patient with variant. The region seems to have good 25-30x coverage with majority of mapping qualities equal to 60. However, apparently there is some other insertion nearby.
The GATK version I am using is 2015.1-3.4.0-1-ga5ca3fc and reference genome is GRCh38.

Could you please explain why the inferred genotype is "./." instead of "0/0" ?

Best,

Ewa

chr1 100474610 rs568102277 T TG 358.91 .
AC=1;AF=0.500;AN=2;BaseQRankSum=2.54;ClippingRankSum=0.419;DB;DP=4026;FS=0.000;MLEAC=1;MLEAF=0.500;MQ=60.00;MQ0=0;MQRankSum=1.36;QD=13.29;ReadPosRankSum=0.814;SOR=0.551
GT:AD:DP:GQ:PGT:PID:PL ./.:36,0:36 ./.:37,0:37
./.:33,0:33 ./.:30,0:30 ./.:36,0:36 ./.:32,0:32
./.:36,0:36 ./.:32,0:32 ./.:31,0:31 ./.:37,0:37
./.:27,0:27 ./.:34,0:34 ./.:38,0:38 ./.:28,0:28
./.:29,0:29 ./.:31,0:31 ./.:25,0:25 ./.:24,0:24
./.:19,0:19 ./.:41,0:41 ./.:24,0:24 ./.:27,0:27 ./.:26,0:26
./.:28,0:28 ./.:31,0:31 ./.:38,0:38 ./.:27,0:27
./.:22,0:22 ./.:31,0:31 ./.:27,0:27 ./.:29,0:29
./.:28,0:28 ./.:34,0:34 ./.:20,0:20 ./.:26,0:26
./.:33,0:33 ./.:26,0:26 ./.:26,0:26 ./.:31,0:31
./.:32,0:32 ./.:34,0:34 ./.:27,0:27 ./.:28,0:28
./.:37,0:37 ./.:38,0:38 ./.:25,0:25 ./.:31,0:31
./.:37,0:37 ./.:31,0:31 ./.:32,0:32 ./.:30,0:30
./.:38,0:38 ./.:36,0:36 ./.:32,0:32 ./.:40,0:40
./.:32,0:32 ./.:42,0:42 ./.:37,0:37 ./.:29,0:29
./.:42,0:42 ./.:31,0:31 ./.:36,0:36 ./.:35,0:35
./.:31,0:31 ./.:35,0:35 ./.:32,0:32 ./.:30,0:30
./.:30,0:30 ./.:36,0:36 ./.:34,0:34 ./.:28,0:28
./.:37,0:37 ./.:34,0:34 ./.:24,0:24 ./.:31,0:31
./.:33,0:33 ./.:36,0:36 ./.:37,0:37 ./.:48,0:48
./.:25,0:25 ./.:39,0:39 ./.:26,0:26 ./.:23,0:23
./.:39,0:39 ./.:29,0:29 ./.:33,0:33 ./.:37,0:37
./.:27,0:27 ./.:29,0:29 ./.:42,0:42 ./.:28,0:28
./.:29,0:29 ./.:30,0:30 ./.:39,0:39 ./.:39,0:39
./.:35,0:35 ./.:31,0:31 ./.:29,0:29 ./.:23,0:23 ./.:30,0:30
./.:24,0:24 ./.:29,0:29 ./.:26,0:26 ./.:19,0:19
./.:26,0:26 ./.:16,0:16 ./.:27,0:27 ./.:24,0:24
./.:34,0:34 ./.:28,0:28 ./.:41,0:41 ./.:41,0:41
./.:39,0:39 ./.:24,0:24
0/1:11,16:27:99:1|0:100474609_G_GT:381,0,245 ./.:36,0:36
./.:26,0:26 ./.:27,0:27 ./.:29,0:29 ./.:29,0:29
./.:28,0:28 ./.:24,0:24 ./.:19,0:19 ./.:31,0:31
./.:33,0:33 ./.:23,0:23 ./.:25,0:25 ./.:31,0:31
./.:34,0:34 ./.:26,0:26

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