rs509613

Variant names:

• chr11-107670211-A-G
• rs509613

Your query was ambiguous. Multiple possible variants found:

• chr11-107670211-A-G
• chr11-107670211-A-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 0.801 in 152,126 control chromosomes in the GnomAD database, including 49,579 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 0.80 (49579 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.548
• Publications: 3 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 (AFR) allele frequency at 95% confidence interval = 0.934 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: 0.801 AC: 121737 AN: 152008 Hom.: 49519 Cov.: 31

Gnomad AFR AF: 0.942

Gnomad AMI AF: 0.719

Gnomad AMR AF: 0.807

Gnomad ASJ AF: 0.706

Gnomad EAS AF: 0.888

Gnomad SAS AF: 0.707

Gnomad FIN AF: 0.777

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.724

Gnomad OTH AF: 0.788

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

GnomAD4 genome AF: 0.801 AC: 121856 AN: 152126 Hom.: 49579 Cov.: 31 AF XY: 0.803 AC XY: 59701 AN XY: 74366

African (AFR) AF: 0.942 AC: 39091 AN: 41512

American (AMR) AF: 0.807 AC: 12336 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.706 AC: 2449 AN: 3470

East Asian (EAS) AF: 0.888 AC: 4582 AN: 5160

South Asian (SAS) AF: 0.707 AC: 3411 AN: 4828

European-Finnish (FIN) AF: 0.777 AC: 8209 AN: 10570

Middle Eastern (MID) AF: 0.728 AC: 214 AN: 294

European-Non Finnish (NFE) AF: 0.724 AC: 49238 AN: 67982

Other (OTH) AF: 0.791 AC: 1670 AN: 2112

Alfa AF: 0.748 Hom.: 181146

Bravo AF: 0.816

Asia WGS AF: 0.810 AC: 2818 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	1.5
DANN	Benign	0.66
PhyloP100		-0.55

Splicing

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

Other links and lift over

dbSNP: rs509613; hg19: chr11-107540937;