10-129101942-C-T

Variant names:

• chr10-129101942-C-T
• rs2039371

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 0.183 in 152,214 control chromosomes in the GnomAD database, including 2,700 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 0.18 (2700 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.835
• Publications: 4 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.23 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: 0.183 AC: 27838 AN: 152096 Hom.: 2696 Cov.: 33

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.134

Gnomad AMR AF: 0.126

Gnomad ASJ AF: 0.166

Gnomad EAS AF: 0.00135

Gnomad SAS AF: 0.0965

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.206

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.183 AC: 27855 AN: 152214 Hom.: 2700 Cov.: 33 AF XY: 0.179 AC XY: 13331 AN XY: 74416

African (AFR) AF: 0.233 AC: 9699 AN: 41540

American (AMR) AF: 0.126 AC: 1924 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 577 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5180

South Asian (SAS) AF: 0.0957 AC: 462 AN: 4826

European-Finnish (FIN) AF: 0.174 AC: 1836 AN: 10578

Middle Eastern (MID) AF: 0.211 AC: 62 AN: 294

European-Non Finnish (NFE) AF: 0.188 AC: 12778 AN: 68006

Other (OTH) AF: 0.184 AC: 388 AN: 2112

Alfa AF: 0.186 Hom.: 1042

Bravo AF: 0.181

Asia WGS AF: 0.0870 AC: 303 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	4.8
DANN	Benign	0.68
PhyloP100		0.83

Splicing

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

Other links and lift over

dbSNP: rs2039371; hg19: chr10-130900206;