10-116417151-C-T

Variant names:

• chr10-116417151-C-T
• rs10749212

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 0.676 in 152,062 control chromosomes in the GnomAD database, including 41,434 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 0.68 (41434 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.259
• Publications: 2 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 (SAS) allele frequency at 95% confidence interval = 0.899 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: 0.676 AC: 102752 AN: 151944 Hom.: 41446 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.920

Gnomad AMR AF: 0.622

Gnomad ASJ AF: 0.918

Gnomad EAS AF: 0.465

Gnomad SAS AF: 0.906

Gnomad FIN AF: 0.895

Gnomad MID AF: 0.892

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.713

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

GnomAD4 genome AF: 0.676 AC: 102743 AN: 152062 Hom.: 41434 Cov.: 32 AF XY: 0.678 AC XY: 50393 AN XY: 74344

African (AFR) AF: 0.234 AC: 9683 AN: 41442

American (AMR) AF: 0.621 AC: 9489 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.918 AC: 3188 AN: 3472

East Asian (EAS) AF: 0.464 AC: 2394 AN: 5156

South Asian (SAS) AF: 0.907 AC: 4369 AN: 4818

European-Finnish (FIN) AF: 0.895 AC: 9477 AN: 10584

Middle Eastern (MID) AF: 0.895 AC: 263 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61542 AN: 68006

Other (OTH) AF: 0.712 AC: 1501 AN: 2108

Alfa AF: 0.835 Hom.: 38621

Bravo AF: 0.627

Asia WGS AF: 0.654 AC: 2277 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	3.4
DANN	Benign	0.61
PhyloP100		0.26

Splicing

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

Other links and lift over

dbSNP: rs10749212; hg19: chr10-118176663;