chr6-31382145-C-T

Variant names:

• chr6-31382145-C-T
• rs9266722

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.154 in 352,166 control chromosomes in the GnomAD database, including 4,839 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 0.14 (1824 hom., cov: 31)
  • Exomes 𝑓: 0.16 (3015 hom.)
• Consequence: HLA-S intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.333
• Publications: 26 publications found

Genes affected

HLA-S (HGNC:19395): (major histocompatibility complex, class I, S (pseudogene))

ENSG00000298426 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.368 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
HLA-S		n.31382145C>T		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
HLA-S	ENST00000425174.1	n.49-67G>A		intron_variant	Intron 1 of 1	6
ENSG00000298426	ENST00000755446.1	n.*157C>T		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21857 AN: 151912 Hom.: 1821 Cov.: 31

Gnomad AFR AF: 0.193

Gnomad AMI AF: 0.0132

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.127

Gnomad EAS AF: 0.383

Gnomad SAS AF: 0.187

Gnomad FIN AF: 0.132

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.101

Gnomad OTH AF: 0.146

GnomAD4 exome AF: 0.162 AC: 32464 AN: 200136 Hom.: 3015 Cov.: 0 AF XY: 0.161 AC XY: 18338 AN XY: 114124

African (AFR) AF: 0.278 AC: 1164 AN: 4180

American (AMR) AF: 0.187 AC: 2698 AN: 14404

Ashkenazi Jewish (ASJ) AF: 0.183 AC: 668 AN: 3642

East Asian (EAS) AF: 0.380 AC: 2970 AN: 7824

South Asian (SAS) AF: 0.186 AC: 6077 AN: 32728

European-Finnish (FIN) AF: 0.149 AC: 3622 AN: 24316

Middle Eastern (MID) AF: 0.127 AC: 276 AN: 2178

European-Non Finnish (NFE) AF: 0.132 AC: 13490 AN: 101820

Other (OTH) AF: 0.166 AC: 1499 AN: 9044

GnomAD4 genome AF: 0.144 AC: 21877 AN: 152030 Hom.: 1824 Cov.: 31 AF XY: 0.149 AC XY: 11097 AN XY: 74330

African (AFR) AF: 0.193 AC: 7976 AN: 41420

American (AMR) AF: 0.130 AC: 1987 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.127 AC: 442 AN: 3470

East Asian (EAS) AF: 0.382 AC: 1978 AN: 5176

South Asian (SAS) AF: 0.187 AC: 898 AN: 4802

European-Finnish (FIN) AF: 0.132 AC: 1393 AN: 10592

Middle Eastern (MID) AF: 0.146 AC: 43 AN: 294

European-Non Finnish (NFE) AF: 0.101 AC: 6834 AN: 67970

Other (OTH) AF: 0.149 AC: 314 AN: 2110

Alfa AF: 0.125 Hom.: 3946

Bravo AF: 0.145

Asia WGS AF: 0.262 AC: 908 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	8.3
DANN	Benign	0.74
PhyloP100		0.33

Splicing

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

Other links and lift over

dbSNP: rs9266722; hg19: chr6-31349922; COSMIC: COSV69645889;