10-28344288-C-T

Variant names:

• chr10-28344288-C-T
• rs1776122

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.197 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

Gnomad4 AFR AF: 0.169

Gnomad4 AMR AF: 0.162

Gnomad4 ASJ AF: 0.210

Gnomad4 EAS AF: 0.0490

Gnomad4 SAS AF: 0.176

Gnomad4 FIN AF: 0.197

Gnomad4 NFE AF: 0.230

Gnomad4 OTH AF: 0.203

Alfa AF: 0.200 Hom.: 1547

Bravo AF: 0.192

Asia WGS AF: 0.111 AC: 387 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

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