rs3181041

chr11-68692436-C-G

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;