10-117774246-T-C

Variant names:

• chr10-117774246-T-C
• rs7088969

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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	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;