10-57539536-C-T

Variant names:

• chr10-57539536-C-T
• rs11005844

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 0.383 in 150,106 control chromosomes in the GnomAD database, including 12,488 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 0.38 (12488 hom., cov: 26)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.59

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.04).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.662 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: 0.383 AC: 57521 AN: 149990 Hom.: 12496 Cov.: 26

Gnomad AFR AF: 0.170

Gnomad AMI AF: 0.564

Gnomad AMR AF: 0.395

Gnomad ASJ AF: 0.468

Gnomad EAS AF: 0.682

Gnomad SAS AF: 0.282

Gnomad FIN AF: 0.481

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.473

Gnomad OTH AF: 0.381

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

GnomAD4 genome AF: 0.383 AC: 57507 AN: 150106 Hom.: 12488 Cov.: 26 AF XY: 0.385 AC XY: 28177 AN XY: 73230

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.395

Gnomad4 ASJ AF: 0.468

Gnomad4 EAS AF: 0.681

Gnomad4 SAS AF: 0.281

Gnomad4 FIN AF: 0.481

Gnomad4 NFE AF: 0.473

Gnomad4 OTH AF: 0.381

Alfa AF: 0.462 Hom.: 25563

Bravo AF: 0.372

Asia WGS AF: 0.426 AC: 1478 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	0.70
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11005844; hg19: chr10-59299296;