rs181652

chr10-117619576-G-Achr10-117619576-G-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 0.494 in 151,906 control chromosomes in the GnomAD database, including 19,221 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 0.49 (19221 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.209

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.645 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: 0.494 AC: 75055 AN: 151788 Hom.: 19229 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.629

Gnomad AMR AF: 0.471

Gnomad ASJ AF: 0.582

Gnomad EAS AF: 0.664

Gnomad SAS AF: 0.623

Gnomad FIN AF: 0.543

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.544

Gnomad OTH AF: 0.528

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

GnomAD4 genome AF: 0.494 AC: 75042 AN: 151906 Hom.: 19221 Cov.: 32 AF XY: 0.497 AC XY: 36890 AN XY: 74222

Gnomad4 AFR AF: 0.359

Gnomad4 AMR AF: 0.470

Gnomad4 ASJ AF: 0.582

Gnomad4 EAS AF: 0.663

Gnomad4 SAS AF: 0.622

Gnomad4 FIN AF: 0.543

Gnomad4 NFE AF: 0.544

Gnomad4 OTH AF: 0.524

Alfa AF: 0.517 Hom.: 11649

Bravo AF: 0.482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.1
Dann	Benign	0.42

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs181652; hg19: chr10-119379087;