rs6902485

Positions:

• chr6-135636654-A-G
• chr6-135636654-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000403495.2(HMGB1P17):​n.60T>C variant causes a non coding transcript exon change. The variant allele was found at a frequency of 0.179 in 169,752 control chromosomes in the GnomAD database, including 6,497 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.19 (6323 hom., cov: 32)
  • Exomes 𝑓: 0.094 (174 hom.)
• Consequence: HMGB1P17 ENST00000403495.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.25

Genes affected

HMGB1P17 (HGNC:39099): (high mobility group box 1 pseudogene 17)

AHI1-DT (HGNC:32526): (AHI1 divergent transcript)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.69).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.532 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
AHI1-DT	NR_152842.1	n.315-5539A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_026805.1	n.201-5539A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152844.1	n.315-5539A>G		intron_variant, non_coding_transcript_variant
AHI1-DT	NR_152845.1	n.439-5539A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
HMGB1P17	ENST00000403495.2	n.60T>C		non_coding_transcript_exon_variant	1/1
AHI1-DT	ENST00000702072.1	n.148-5539A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28646 AN: 152000 Hom.: 6310 Cov.: 32

Gnomad AFR AF: 0.538

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.131

Gnomad ASJ AF: 0.101

Gnomad EAS AF: 0.0493

Gnomad SAS AF: 0.0743

Gnomad FIN AF: 0.00622

Gnomad MID AF: 0.142

Gnomad NFE AF: 0.0435

Gnomad OTH AF: 0.191

GnomAD4 exome AF: 0.0942 AC: 1662 AN: 17634 Hom.: 174 Cov.: 0 AF XY: 0.0906 AC XY: 977 AN XY: 10780

Gnomad4 AFR exome AF: 0.636

Gnomad4 AMR exome AF: 0.138

Gnomad4 ASJ exome AF: 0.136

Gnomad4 EAS exome AF: 0.0643

Gnomad4 SAS exome AF: 0.121

Gnomad4 FIN exome AF: 0.0118

Gnomad4 NFE exome AF: 0.0613

Gnomad4 OTH exome AF: 0.0607

GnomAD4 genome AF: 0.189 AC: 28713 AN: 152118 Hom.: 6323 Cov.: 32 AF XY: 0.182 AC XY: 13551 AN XY: 74356

Gnomad4 AFR AF: 0.538

Gnomad4 AMR AF: 0.130

Gnomad4 ASJ AF: 0.101

Gnomad4 EAS AF: 0.0492

Gnomad4 SAS AF: 0.0745

Gnomad4 FIN AF: 0.00622

Gnomad4 NFE AF: 0.0434

Gnomad4 OTH AF: 0.195

Alfa AF: 0.0607 Hom.: 1005

Bravo AF: 0.214

Asia WGS AF: 0.122 AC: 422 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.69
CADD	Benign	2.2
DANN	Benign	0.36

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs6902485; hg19: chr6-135957792;