11-57238113-T-C

Variant names:

• chr11-57238113-T-C
• rs10501367

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 0.731 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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.731 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

Gnomad4 AFR AF: 0.710

Gnomad4 AMR AF: 0.762

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.776

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.796

Gnomad4 NFE AF: 0.716

Gnomad4 OTH AF: 0.745

Alfa AF: 0.719 Hom.: 51291

Bravo AF: 0.725

Asia WGS AF: 0.823 AC: 2860 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10501367; hg19: chr11-57005587;