rs11694911

chr2-10433072-C-T

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 0.122 in 151,606 control chromosomes in the GnomAD database, including 1,267 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 0.12 (1267 hom., cov: 34)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.609

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.317 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: 0.122 AC: 18412 AN: 151486 Hom.: 1265 Cov.: 34

Gnomad AFR AF: 0.0995

Gnomad AMI AF: 0.226

Gnomad AMR AF: 0.119

Gnomad ASJ AF: 0.120

Gnomad EAS AF: 0.331

Gnomad SAS AF: 0.181

Gnomad FIN AF: 0.167

Gnomad MID AF: 0.155

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.112

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

GnomAD4 genome AF: 0.122 AC: 18421 AN: 151606 Hom.: 1267 Cov.: 34 AF XY: 0.126 AC XY: 9372 AN XY: 74120

Gnomad4 AFR AF: 0.0996

Gnomad4 AMR AF: 0.118

Gnomad4 ASJ AF: 0.120

Gnomad4 EAS AF: 0.330

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.167

Gnomad4 NFE AF: 0.107

Gnomad4 OTH AF: 0.115

Alfa AF: 0.110 Hom.: 1279

Bravo AF: 0.115

Asia WGS AF: 0.237 AC: 821 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	2.7
Dann	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11694911; hg19: chr2-10573198;