rs341076

Variant names:

• chr11-72546874-G-A
• rs341076

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 0.638 in 151,906 control chromosomes in the GnomAD database, including 31,626 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 0.64 (31626 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.472
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.68).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.724 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: 0.638 AC: 96906 AN: 151788 Hom.: 31618 Cov.: 32

Gnomad AFR AF: 0.493

Gnomad AMI AF: 0.706

Gnomad AMR AF: 0.719

Gnomad ASJ AF: 0.697

Gnomad EAS AF: 0.671

Gnomad SAS AF: 0.744

Gnomad FIN AF: 0.669

Gnomad MID AF: 0.731

Gnomad NFE AF: 0.689

Gnomad OTH AF: 0.668

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

GnomAD4 genome AF: 0.638 AC: 96954 AN: 151906 Hom.: 31626 Cov.: 32 AF XY: 0.639 AC XY: 47433 AN XY: 74240

African (AFR) AF: 0.493 AC: 20393 AN: 41396

American (AMR) AF: 0.719 AC: 10987 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.697 AC: 2418 AN: 3470

East Asian (EAS) AF: 0.670 AC: 3456 AN: 5156

South Asian (SAS) AF: 0.744 AC: 3585 AN: 4816

European-Finnish (FIN) AF: 0.669 AC: 7054 AN: 10540

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

European-Non Finnish (NFE) AF: 0.689 AC: 46793 AN: 67938

Other (OTH) AF: 0.668 AC: 1413 AN: 2114

Alfa AF: 0.665 Hom.: 12888

Bravo AF: 0.637

Asia WGS AF: 0.709 AC: 2466 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	2.0
DANN	Benign	0.76
PhyloP100		-0.47

Splicing

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

Other links and lift over

dbSNP: rs341076; hg19: chr11-72257918;