rs3181041

Variant names:

• chr11-68692436-C-G
• rs3181041

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 0.0775 in 152,240 control chromosomes in the GnomAD database, including 594 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 0.077 (594 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0650

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.1 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: 0.0776 AC: 11798 AN: 152122 Hom.: 596 Cov.: 31

Gnomad AFR AF: 0.0246

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.0928

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.0225

Gnomad SAS AF: 0.0276

Gnomad FIN AF: 0.0873

Gnomad MID AF: 0.114

Gnomad NFE AF: 0.102

Gnomad OTH AF: 0.103

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

GnomAD4 genome AF: 0.0775 AC: 11794 AN: 152240 Hom.: 594 Cov.: 31 AF XY: 0.0748 AC XY: 5571 AN XY: 74468

Gnomad4 AFR AF: 0.0246

Gnomad4 AMR AF: 0.0925

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.0228

Gnomad4 SAS AF: 0.0274

Gnomad4 FIN AF: 0.0873

Gnomad4 NFE AF: 0.102

Gnomad4 OTH AF: 0.101

Alfa AF: 0.0884 Hom.: 91

Bravo AF: 0.0787

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.24
DANN	Benign	0.65

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs3181041; hg19: chr11-68459904;