10-3959705-C-T

Position:

• chr10-3959705-C-T

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 0.13 in 152,150 control chromosomes in the GnomAD database, including 1,748 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 0.13 (1748 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.555

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.185 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.130 AC: 19729 AN: 152032 Hom.: 1751 Cov.: 32

Gnomad AFR AF: 0.0327

Gnomad AMI AF: 0.459

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.235

Gnomad EAS AF: 0.0370

Gnomad SAS AF: 0.107

Gnomad FIN AF: 0.0983

Gnomad MID AF: 0.197

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.167

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

GnomAD4 genome AF: 0.130 AC: 19718 AN: 152150 Hom.: 1748 Cov.: 32 AF XY: 0.125 AC XY: 9258 AN XY: 74360

Gnomad4 AFR AF: 0.0326

Gnomad4 AMR AF: 0.145

Gnomad4 ASJ AF: 0.235

Gnomad4 EAS AF: 0.0373

Gnomad4 SAS AF: 0.106

Gnomad4 FIN AF: 0.0983

Gnomad4 NFE AF: 0.188

Gnomad4 OTH AF: 0.166

Alfa AF: 0.179 Hom.: 5291

Bravo AF: 0.131

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2031573; hg19: chr10-4001897;