chr10-28344288-C-T

Variant names:

• chr10-28344288-C-T
• rs1776122

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 0.197 in 151,902 control chromosomes in the GnomAD database, including 3,077 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 0.20 (3077 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.458
• Publications: 6 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.71).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.227 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: 0.197 AC: 29887 AN: 151784 Hom.: 3073 Cov.: 32

Gnomad AFR AF: 0.169

Gnomad AMI AF: 0.439

Gnomad AMR AF: 0.162

Gnomad ASJ AF: 0.210

Gnomad EAS AF: 0.0491

Gnomad SAS AF: 0.174

Gnomad FIN AF: 0.197

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.230

Gnomad OTH AF: 0.204

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

GnomAD4 genome AF: 0.197 AC: 29916 AN: 151902 Hom.: 3077 Cov.: 32 AF XY: 0.194 AC XY: 14439 AN XY: 74238

African (AFR) AF: 0.169 AC: 7017 AN: 41446

American (AMR) AF: 0.162 AC: 2472 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.210 AC: 730 AN: 3468

East Asian (EAS) AF: 0.0490 AC: 253 AN: 5164

South Asian (SAS) AF: 0.176 AC: 846 AN: 4812

European-Finnish (FIN) AF: 0.197 AC: 2074 AN: 10530

Middle Eastern (MID) AF: 0.180 AC: 53 AN: 294

European-Non Finnish (NFE) AF: 0.230 AC: 15649 AN: 67916

Other (OTH) AF: 0.203 AC: 427 AN: 2108

Alfa AF: 0.202 Hom.: 1736

Bravo AF: 0.192

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.71
CADD	Benign	5.8
DANN	Benign	0.90
PhyloP100		-0.46

Splicing

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

Other links and lift over

dbSNP: rs1776122; hg19: chr10-28633217; COSMIC: COSV71214722;