10-130949624-C-T

Position:

• chr10-130949624-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 0.151 in 152,176 control chromosomes in the GnomAD database, including 1,978 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 0.15 (1978 hom., cov: 33)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.377 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: 0.151 AC: 22931 AN: 152056 Hom.: 1981 Cov.: 33

Gnomad AFR AF: 0.123

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.122

Gnomad ASJ AF: 0.121

Gnomad EAS AF: 0.392

Gnomad SAS AF: 0.153

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.108

Gnomad NFE AF: 0.150

Gnomad OTH AF: 0.142

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

GnomAD4 genome AF: 0.151 AC: 22937 AN: 152176 Hom.: 1978 Cov.: 33 AF XY: 0.153 AC XY: 11353 AN XY: 74384

Gnomad4 AFR AF: 0.123

Gnomad4 AMR AF: 0.122

Gnomad4 ASJ AF: 0.121

Gnomad4 EAS AF: 0.392

Gnomad4 SAS AF: 0.152

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.150

Gnomad4 OTH AF: 0.143

Alfa AF: 0.151 Hom.: 1545

Bravo AF: 0.145

Asia WGS AF: 0.245 AC: 850 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.9
DANN	Benign	0.52

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10829848; hg19: chr10-132747887;