chr11-57238113-T-C

Position:

• chr11-57238113-T-C

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;