10-117902581-T-C

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 0.832 in 152,070 control chromosomes in the GnomAD database, including 52,622 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 0.83 (52622 hom., cov: 30)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.60

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 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: 0.832 AC: 126369 AN: 151952 Hom.: 52584 Cov.: 30

Gnomad AFR AF: 0.810

Gnomad AMI AF: 0.844

Gnomad AMR AF: 0.837

Gnomad ASJ AF: 0.801

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.860

Gnomad FIN AF: 0.885

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.827

Gnomad OTH AF: 0.822

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

GnomAD4 genome AF: 0.832 AC: 126456 AN: 152070 Hom.: 52622 Cov.: 30 AF XY: 0.836 AC XY: 62152 AN XY: 74312

Gnomad4 AFR AF: 0.809

Gnomad4 AMR AF: 0.837

Gnomad4 ASJ AF: 0.801

Gnomad4 EAS AF: 0.947

Gnomad4 SAS AF: 0.861

Gnomad4 FIN AF: 0.885

Gnomad4 NFE AF: 0.826

Gnomad4 OTH AF: 0.825

Alfa AF: 0.820 Hom.: 49834

Bravo AF: 0.828

Asia WGS AF: 0.890 AC: 3095 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.053
Dann	Benign	0.20

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1936295; hg19: chr10-119662092;