6-32739518-G-T

Variant names:

• chr6-32739518-G-T
• rs9276370

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 0.52 in 151,936 control chromosomes in the GnomAD database, including 21,942 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 0.52 (21942 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.111
• Publications: 42 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.520 AC: 78924 AN: 151818 Hom.: 21922 Cov.: 31

Gnomad AFR AF: 0.334

Gnomad AMI AF: 0.731

Gnomad AMR AF: 0.598

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.850

Gnomad SAS AF: 0.786

Gnomad FIN AF: 0.583

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.555

Gnomad OTH AF: 0.556

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.520 AC: 78981 AN: 151936 Hom.: 21942 Cov.: 31 AF XY: 0.529 AC XY: 39291 AN XY: 74266

African (AFR) AF: 0.334 AC: 13820 AN: 41410

American (AMR) AF: 0.598 AC: 9135 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1969 AN: 3468

East Asian (EAS) AF: 0.850 AC: 4409 AN: 5186

South Asian (SAS) AF: 0.787 AC: 3793 AN: 4822

European-Finnish (FIN) AF: 0.583 AC: 6135 AN: 10532

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.555 AC: 37687 AN: 67928

Other (OTH) AF: 0.562 AC: 1185 AN: 2108

Alfa AF: 0.542 Hom.: 93111

Bravo AF: 0.512

Asia WGS AF: 0.777 AC: 2697 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	6.2
DANN	Benign	0.54
PhyloP100		0.11

Splicing

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

Other links and lift over

dbSNP: rs9276370; hg19: chr6-32707295;