chr11-57237593-T-C

Position:

• chr11-57237593-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 0.633 in 151,960 control chromosomes in the GnomAD database, including 30,845 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 0.63 (30845 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.205

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.7).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.748 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: 0.633 AC: 96139 AN: 151842 Hom.: 30797 Cov.: 32

Gnomad AFR AF: 0.684

Gnomad AMI AF: 0.574

Gnomad AMR AF: 0.662

Gnomad ASJ AF: 0.660

Gnomad EAS AF: 0.769

Gnomad SAS AF: 0.721

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.642

Gnomad NFE AF: 0.574

Gnomad OTH AF: 0.644

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

GnomAD4 genome AF: 0.633 AC: 96253 AN: 151960 Hom.: 30845 Cov.: 32 AF XY: 0.641 AC XY: 47591 AN XY: 74278

Gnomad4 AFR AF: 0.685

Gnomad4 AMR AF: 0.662

Gnomad4 ASJ AF: 0.660

Gnomad4 EAS AF: 0.768

Gnomad4 SAS AF: 0.721

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.574

Gnomad4 OTH AF: 0.647

Alfa AF: 0.590 Hom.: 52805

Bravo AF: 0.632

Asia WGS AF: 0.780 AC: 2711 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.70
CADD	Benign	14
DANN	Benign	0.77

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9943582; hg19: chr11-57005067;