11-69048055-C-T

Variant names:

• chr11-69048055-C-T
• rs10750836

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 0.77 in 152,088 control chromosomes in the GnomAD database, including 50,561 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 0.77 (50561 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.988
• Publications: 12 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.982 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.770 AC: 117087 AN: 151970 Hom.: 50570 Cov.: 32

Gnomad AFR AF: 0.388

Gnomad AMI AF: 0.987

Gnomad AMR AF: 0.661

Gnomad ASJ AF: 0.984

Gnomad EAS AF: 0.540

Gnomad SAS AF: 0.883

Gnomad FIN AF: 0.978

Gnomad MID AF: 0.937

Gnomad NFE AF: 0.989

Gnomad OTH AF: 0.812

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

GnomAD4 genome AF: 0.770 AC: 117101 AN: 152088 Hom.: 50561 Cov.: 32 AF XY: 0.768 AC XY: 57103 AN XY: 74346

African (AFR) AF: 0.388 AC: 16071 AN: 41440

American (AMR) AF: 0.660 AC: 10073 AN: 15254

Ashkenazi Jewish (ASJ) AF: 0.984 AC: 3415 AN: 3470

East Asian (EAS) AF: 0.539 AC: 2778 AN: 5154

South Asian (SAS) AF: 0.884 AC: 4263 AN: 4824

European-Finnish (FIN) AF: 0.978 AC: 10383 AN: 10612

Middle Eastern (MID) AF: 0.939 AC: 276 AN: 294

European-Non Finnish (NFE) AF: 0.989 AC: 67234 AN: 68016

Other (OTH) AF: 0.809 AC: 1710 AN: 2114

Alfa AF: 0.898 Hom.: 150677

Bravo AF: 0.727

Asia WGS AF: 0.697 AC: 2427 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.84
DANN	Benign	0.84
PhyloP100		-0.99

Splicing

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

Other links and lift over

dbSNP: rs10750836; hg19: chr11-68815523;