11-57238113-T-C

Variant names:

• chr11-57238113-T-C
• rs10501367

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 0.731 in 152,158 control chromosomes in the GnomAD database, including 40,799 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 0.73 (40799 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.06
• Publications: 24 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.777 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: 0.731 AC: 111087 AN: 152040 Hom.: 40752 Cov.: 33

Gnomad AFR AF: 0.709

Gnomad AMI AF: 0.692

Gnomad AMR AF: 0.762

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.776

Gnomad SAS AF: 0.798

Gnomad FIN AF: 0.796

Gnomad MID AF: 0.782

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.743

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

GnomAD4 genome AF: 0.731 AC: 111199 AN: 152158 Hom.: 40799 Cov.: 33 AF XY: 0.736 AC XY: 54788 AN XY: 74400

African (AFR) AF: 0.710 AC: 29431 AN: 41470

American (AMR) AF: 0.762 AC: 11660 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2653 AN: 3472

East Asian (EAS) AF: 0.776 AC: 4011 AN: 5172

South Asian (SAS) AF: 0.798 AC: 3855 AN: 4830

European-Finnish (FIN) AF: 0.796 AC: 8434 AN: 10594

Middle Eastern (MID) AF: 0.796 AC: 234 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48715 AN: 68006

Other (OTH) AF: 0.745 AC: 1576 AN: 2116

Alfa AF: 0.722 Hom.: 72222

Bravo AF: 0.725

Asia WGS AF: 0.823 AC: 2860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.63
DANN	Benign	0.28
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs10501367; hg19: chr11-57005587;