10-117774246-T-C

Position:

• chr10-117774246-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.599 in 150,550 control chromosomes in the GnomAD database, including 27,536 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 0.60 (27536 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.38).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.677 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: 0.600 AC: 90203 AN: 150438 Hom.: 27524 Cov.: 32

Gnomad AFR AF: 0.481

Gnomad AMI AF: 0.928

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.599

Gnomad EAS AF: 0.436

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.627

Gnomad MID AF: 0.522

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.602

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

GnomAD4 genome AF: 0.599 AC: 90242 AN: 150550 Hom.: 27536 Cov.: 32 AF XY: 0.594 AC XY: 43727 AN XY: 73572

Gnomad4 AFR AF: 0.481

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.599

Gnomad4 EAS AF: 0.436

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.627

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.603

Alfa AF: 0.648 Hom.: 31656

Bravo AF: 0.583

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7088969; hg19: chr10-119533757;