rs9274759

Variant names:

• chr6-32670538-G-A
• rs9274759

Your query was ambiguous. Multiple possible variants found:

• chr6-32670538-G-A
• chr6-32670538-G-C
• chr6-32670538-G-T

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 0.471 in 148,490 control chromosomes in the GnomAD database, including 18,894 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 0.47 (18894 hom., cov: 29)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.619
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.739 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: 0.472 AC: 69963 AN: 148374 Hom.: 18887 Cov.: 29

Gnomad AFR AF: 0.461

Gnomad AMI AF: 0.478

Gnomad AMR AF: 0.580

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.759

Gnomad SAS AF: 0.548

Gnomad FIN AF: 0.426

Gnomad MID AF: 0.570

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.490

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

GnomAD4 genome AF: 0.471 AC: 70006 AN: 148490 Hom.: 18894 Cov.: 29 AF XY: 0.475 AC XY: 34387 AN XY: 72416

African (AFR) AF: 0.461 AC: 18939 AN: 41066

American (AMR) AF: 0.580 AC: 8551 AN: 14736

Ashkenazi Jewish (ASJ) AF: 0.547 AC: 1799 AN: 3286

East Asian (EAS) AF: 0.759 AC: 3812 AN: 5024

South Asian (SAS) AF: 0.545 AC: 2493 AN: 4576

European-Finnish (FIN) AF: 0.426 AC: 4400 AN: 10326

Middle Eastern (MID) AF: 0.552 AC: 139 AN: 252

European-Non Finnish (NFE) AF: 0.429 AC: 28445 AN: 66308

Other (OTH) AF: 0.495 AC: 1012 AN: 2046

Alfa AF: 0.446 Hom.: 4541

Asia WGS AF: 0.638 AC: 2188 AN: 3434

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	1.5
DANN	Benign	0.29
PhyloP100		-0.62

Splicing

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

Other links and lift over

dbSNP: rs9274759; hg19: chr6-32638315;