10-117554396-T-C

Variant names:

• chr10-117554396-T-C
• rs242960

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.752 in 152,110 control chromosomes in the GnomAD database, including 43,300 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 0.75 (43300 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.68
• Publications: 1 publications found

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.805 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: 0.752 AC: 114363 AN: 151992 Hom.: 43276 Cov.: 32

Gnomad AFR AF: 0.812

Gnomad AMI AF: 0.668

Gnomad AMR AF: 0.738

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.799

Gnomad SAS AF: 0.573

Gnomad FIN AF: 0.709

Gnomad MID AF: 0.741

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.780

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

GnomAD4 genome AF: 0.752 AC: 114438 AN: 152110 Hom.: 43300 Cov.: 32 AF XY: 0.747 AC XY: 55532 AN XY: 74360

African (AFR) AF: 0.812 AC: 33704 AN: 41514

American (AMR) AF: 0.737 AC: 11262 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2325 AN: 3470

East Asian (EAS) AF: 0.800 AC: 4114 AN: 5144

South Asian (SAS) AF: 0.574 AC: 2768 AN: 4826

European-Finnish (FIN) AF: 0.709 AC: 7503 AN: 10580

Middle Eastern (MID) AF: 0.735 AC: 216 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50290 AN: 67982

Other (OTH) AF: 0.781 AC: 1647 AN: 2108

Alfa AF: 0.727 Hom.: 3296

Bravo AF: 0.765

Asia WGS AF: 0.683 AC: 2378 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.11
DANN	Benign	0.29
PhyloP100		-1.7

Splicing

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

Other links and lift over

dbSNP: rs242960; hg19: chr10-119313907;