rs7941541

chr11-86147496-G-Achr11-86147496-G-C

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 0.728 in 152,132 control chromosomes in the GnomAD database, including 40,932 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 0.73 (40932 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.728 AC: 110645 AN: 152012 Hom.: 40890 Cov.: 32

Gnomad AFR AF: 0.869

Gnomad AMI AF: 0.599

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.692

Gnomad EAS AF: 0.590

Gnomad SAS AF: 0.653

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.649

Gnomad NFE AF: 0.686

Gnomad OTH AF: 0.724

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

GnomAD4 genome AF: 0.728 AC: 110744 AN: 152132 Hom.: 40932 Cov.: 32 AF XY: 0.724 AC XY: 53806 AN XY: 74364

Gnomad4 AFR AF: 0.870

Gnomad4 AMR AF: 0.668

Gnomad4 ASJ AF: 0.692

Gnomad4 EAS AF: 0.589

Gnomad4 SAS AF: 0.654

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.686

Gnomad4 OTH AF: 0.723

Alfa AF: 0.693 Hom.: 55271

Bravo AF: 0.734

Asia WGS AF: 0.611 AC: 2124 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	2.3
Dann	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7941541; hg19: chr11-85858538;