rs10895959

Variant names:

• chr11-106459435-G-A
• rs10895959

Your query was ambiguous. Multiple possible variants found:

• chr11-106459435-G-A
• chr11-106459435-G-T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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

African (AFR) AF: 0.825 AC: 34254 AN: 41528

American (AMR) AF: 0.642 AC: 9803 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.616 AC: 2140 AN: 3472

East Asian (EAS) AF: 0.428 AC: 2205 AN: 5156

South Asian (SAS) AF: 0.571 AC: 2753 AN: 4822

European-Finnish (FIN) AF: 0.624 AC: 6595 AN: 10564

Middle Eastern (MID) AF: 0.782 AC: 230 AN: 294

European-Non Finnish (NFE) AF: 0.571 AC: 38813 AN: 67936

Other (OTH) AF: 0.676 AC: 1427 AN: 2112

Alfa AF: 0.599 Hom.: 62193

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
PhyloP100		0.34

Splicing

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

Other links and lift over

dbSNP: rs10895959; hg19: chr11-106330162;