chr10-129102125-T-C

Variant names:

• chr10-129102125-T-C
• rs2039372

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 152,252 control chromosomes in the GnomAD database, including 2,695 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 (2695 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.316
• Publications: 4 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.229 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: 27834 AN: 152136 Hom.: 2691 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: 0.0955

Gnomad FIN AF: 0.173

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.188

Gnomad OTH AF: 0.178

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

GnomAD4 genome AF: 0.183 AC: 27850 AN: 152252 Hom.: 2695 Cov.: 33 AF XY: 0.179 AC XY: 13341 AN XY: 74464

African (AFR) AF: 0.233 AC: 9689 AN: 41518

American (AMR) AF: 0.126 AC: 1928 AN: 15308

Ashkenazi Jewish (ASJ) AF: 0.166 AC: 576 AN: 3470

East Asian (EAS) AF: 0.00135 AC: 7 AN: 5186

South Asian (SAS) AF: 0.0948 AC: 457 AN: 4822

European-Finnish (FIN) AF: 0.173 AC: 1838 AN: 10614

Middle Eastern (MID) AF: 0.212 AC: 62 AN: 292

European-Non Finnish (NFE) AF: 0.188 AC: 12784 AN: 68018

Other (OTH) AF: 0.183 AC: 387 AN: 2112

Alfa AF: 0.182 Hom.: 4346

Bravo AF: 0.181

Asia WGS AF: 0.0880 AC: 304 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	1.2
DANN	Benign	0.55
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs2039372; hg19: chr10-130900389;