10-3959705-C-T

Variant names:

• chr10-3959705-C-T
• rs2031573

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 11 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.0326 AC: 1355 AN: 41530

American (AMR) AF: 0.145 AC: 2211 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.235 AC: 816 AN: 3466

East Asian (EAS) AF: 0.0373 AC: 193 AN: 5174

South Asian (SAS) AF: 0.106 AC: 512 AN: 4810

European-Finnish (FIN) AF: 0.0983 AC: 1039 AN: 10570

Middle Eastern (MID) AF: 0.195 AC: 57 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12766 AN: 68000

Other (OTH) AF: 0.166 AC: 350 AN: 2110

Alfa AF: 0.170 Hom.: 10580

Bravo AF: 0.131

Asia WGS AF: 0.0770 AC: 267 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.1
DANN	Benign	0.68
PhyloP100		-0.56

Splicing

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

Other links and lift over

dbSNP: rs2031573; hg19: chr10-4001897;