10-113182606-C-A

Position:

• chr10-113182606-C-A

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 0.402 in 152,042 control chromosomes in the GnomAD database, including 16,100 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 0.40 (16100 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.199

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.736 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: 0.402 AC: 61017 AN: 151924 Hom.: 16049 Cov.: 32

Gnomad AFR AF: 0.724

Gnomad AMI AF: 0.167

Gnomad AMR AF: 0.349

Gnomad ASJ AF: 0.265

Gnomad EAS AF: 0.755

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.213

Gnomad MID AF: 0.332

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.382

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

GnomAD4 genome AF: 0.402 AC: 61130 AN: 152042 Hom.: 16100 Cov.: 32 AF XY: 0.402 AC XY: 29871 AN XY: 74316

Gnomad4 AFR AF: 0.724

Gnomad4 AMR AF: 0.349

Gnomad4 ASJ AF: 0.265

Gnomad4 EAS AF: 0.756

Gnomad4 SAS AF: 0.472

Gnomad4 FIN AF: 0.213

Gnomad4 NFE AF: 0.226

Gnomad4 OTH AF: 0.385

Alfa AF: 0.321 Hom.: 1738

Bravo AF: 0.425

Asia WGS AF: 0.634 AC: 2204 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.46
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7915609; hg19: chr10-114942365;