rs9276490

Variant names:

• chr6-32750904-A-G
• rs9276490

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 0.617 in 151,950 control chromosomes in the GnomAD database, including 29,338 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 0.62 (29338 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637
• Publications: 19 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.794 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.617 AC: 93626 AN: 151830 Hom.: 29301 Cov.: 32

Gnomad AFR AF: 0.644

Gnomad AMI AF: 0.733

Gnomad AMR AF: 0.683

Gnomad ASJ AF: 0.642

Gnomad EAS AF: 0.815

Gnomad SAS AF: 0.697

Gnomad FIN AF: 0.582

Gnomad MID AF: 0.669

Gnomad NFE AF: 0.565

Gnomad OTH AF: 0.671

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

GnomAD4 genome AF: 0.617 AC: 93722 AN: 151950 Hom.: 29338 Cov.: 32 AF XY: 0.622 AC XY: 46214 AN XY: 74266

African (AFR) AF: 0.644 AC: 26675 AN: 41428

American (AMR) AF: 0.683 AC: 10442 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.642 AC: 2226 AN: 3468

East Asian (EAS) AF: 0.814 AC: 4222 AN: 5184

South Asian (SAS) AF: 0.697 AC: 3357 AN: 4818

European-Finnish (FIN) AF: 0.582 AC: 6133 AN: 10532

Middle Eastern (MID) AF: 0.682 AC: 199 AN: 292

European-Non Finnish (NFE) AF: 0.565 AC: 38376 AN: 67930

Other (OTH) AF: 0.676 AC: 1425 AN: 2108

Alfa AF: 0.575 Hom.: 53521

Bravo AF: 0.630

Asia WGS AF: 0.725 AC: 2515 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	2.9
DANN	Benign	0.38
PhyloP100		-0.64

Splicing

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

Other links and lift over

dbSNP: rs9276490; hg19: chr6-32718681;