10-117774246-T-C

Variant names:

• chr10-117774246-T-C
• rs7088969

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 publications found

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

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

African (AFR) AF: 0.481 AC: 19231 AN: 40010

American (AMR) AF: 0.559 AC: 8528 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.599 AC: 2077 AN: 3468

East Asian (EAS) AF: 0.436 AC: 2250 AN: 5160

South Asian (SAS) AF: 0.593 AC: 2858 AN: 4818

European-Finnish (FIN) AF: 0.627 AC: 6628 AN: 10570

Middle Eastern (MID) AF: 0.527 AC: 155 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46408 AN: 67982

Other (OTH) AF: 0.603 AC: 1261 AN: 2092

Alfa AF: 0.630 Hom.: 47311

Bravo AF: 0.583

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.38
CADD	Benign	15
DANN	Benign	0.59
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs7088969; hg19: chr10-119533757;