rs9276598

Variant names:

• chr6-32766210-G-A
• rs9276598

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 0.554 in 151,906 control chromosomes in the GnomAD database, including 23,746 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 0.55 (23746 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0960
• Publications: 18 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 = 0.69 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: 0.554 AC: 84109 AN: 151788 Hom.: 23730 Cov.: 31

Gnomad AFR AF: 0.618

Gnomad AMI AF: 0.684

Gnomad AMR AF: 0.587

Gnomad ASJ AF: 0.561

Gnomad EAS AF: 0.709

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.583

Gnomad NFE AF: 0.492

Gnomad OTH AF: 0.596

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

GnomAD4 genome AF: 0.554 AC: 84180 AN: 151906 Hom.: 23746 Cov.: 31 AF XY: 0.558 AC XY: 41431 AN XY: 74216

African (AFR) AF: 0.618 AC: 25610 AN: 41430

American (AMR) AF: 0.587 AC: 8970 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.561 AC: 1940 AN: 3456

East Asian (EAS) AF: 0.709 AC: 3654 AN: 5154

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4812

European-Finnish (FIN) AF: 0.542 AC: 5708 AN: 10530

Middle Eastern (MID) AF: 0.603 AC: 176 AN: 292

European-Non Finnish (NFE) AF: 0.491 AC: 33388 AN: 67932

Other (OTH) AF: 0.603 AC: 1269 AN: 2106

Alfa AF: 0.515 Hom.: 72434

Bravo AF: 0.567

Asia WGS AF: 0.621 AC: 2158 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	4.0
DANN	Benign	0.68
PhyloP100		-0.096

Splicing

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

Other links and lift over

dbSNP: rs9276598; hg19: chr6-32733987;