rs10895959

chr11-106459435-G-Achr11-106459435-G-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 0.65 in 152,070 control chromosomes in the GnomAD database, including 33,279 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 0.65 (33279 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.341

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.818 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: 0.650 AC: 98723 AN: 151952 Hom.: 33221 Cov.: 33

Gnomad AFR AF: 0.824

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.643

Gnomad ASJ AF: 0.616

Gnomad EAS AF: 0.427

Gnomad SAS AF: 0.571

Gnomad FIN AF: 0.624

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.571

Gnomad OTH AF: 0.676

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

GnomAD4 genome AF: 0.650 AC: 98828 AN: 152070 Hom.: 33279 Cov.: 33 AF XY: 0.650 AC XY: 48322 AN XY: 74310

Gnomad4 AFR AF: 0.825

Gnomad4 AMR AF: 0.642

Gnomad4 ASJ AF: 0.616

Gnomad4 EAS AF: 0.428

Gnomad4 SAS AF: 0.571

Gnomad4 FIN AF: 0.624

Gnomad4 NFE AF: 0.571

Gnomad4 OTH AF: 0.676

Alfa AF: 0.582 Hom.: 34098

Bravo AF: 0.658

Asia WGS AF: 0.495 AC: 1723 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	2.2
Dann	Benign	0.29

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10895959; hg19: chr11-106330162;