10-118413126-G-T

Variant names:

• chr10-118413126-G-T
• rs1857269

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 0.389 in 151,868 control chromosomes in the GnomAD database, including 11,847 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 0.39 (11847 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.35
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.48).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.604 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: 0.390 AC: 59119 AN: 151754 Hom.: 11845 Cov.: 31

Gnomad AFR AF: 0.347

Gnomad AMI AF: 0.327

Gnomad AMR AF: 0.319

Gnomad ASJ AF: 0.390

Gnomad EAS AF: 0.622

Gnomad SAS AF: 0.446

Gnomad FIN AF: 0.534

Gnomad MID AF: 0.310

Gnomad NFE AF: 0.389

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.389 AC: 59147 AN: 151868 Hom.: 11847 Cov.: 31 AF XY: 0.398 AC XY: 29547 AN XY: 74182

African (AFR) AF: 0.347 AC: 14370 AN: 41388

American (AMR) AF: 0.318 AC: 4862 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.390 AC: 1352 AN: 3468

East Asian (EAS) AF: 0.622 AC: 3207 AN: 5160

South Asian (SAS) AF: 0.446 AC: 2148 AN: 4812

European-Finnish (FIN) AF: 0.534 AC: 5623 AN: 10524

Middle Eastern (MID) AF: 0.286 AC: 84 AN: 294

European-Non Finnish (NFE) AF: 0.389 AC: 26412 AN: 67934

Other (OTH) AF: 0.375 AC: 791 AN: 2108

Alfa AF: 0.385 Hom.: 48359

Bravo AF: 0.368

Asia WGS AF: 0.504 AC: 1756 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.48
CADD	Benign	19
DANN	Benign	0.82
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs1857269; hg19: chr10-120172638;