rs341076

Variant names:

• chr11-72546874-G-A
• rs341076

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.493

Gnomad4 AMR AF: 0.719

Gnomad4 ASJ AF: 0.697

Gnomad4 EAS AF: 0.670

Gnomad4 SAS AF: 0.744

Gnomad4 FIN AF: 0.669

Gnomad4 NFE AF: 0.689

Gnomad4 OTH AF: 0.668

Alfa AF: 0.665 Hom.: 7215

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs341076; hg19: chr11-72257918;