chr10-81429424-C-T

Variant names:

• chr10-81429424-C-T
• rs4933782

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 0.204 in 151,566 control chromosomes in the GnomAD database, including 3,678 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 (3678 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.765

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.204 AC: 30902 AN: 151446 Hom.: 3670 Cov.: 32

Gnomad AFR AF: 0.112

Gnomad AMI AF: 0.293

Gnomad AMR AF: 0.266

Gnomad ASJ AF: 0.205

Gnomad EAS AF: 0.478

Gnomad SAS AF: 0.364

Gnomad FIN AF: 0.276

Gnomad MID AF: 0.176

Gnomad NFE AF: 0.202

Gnomad OTH AF: 0.196

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

GnomAD4 genome AF: 0.204 AC: 30922 AN: 151566 Hom.: 3678 Cov.: 32 AF XY: 0.213 AC XY: 15735 AN XY: 74030

Gnomad4 AFR AF: 0.112

Gnomad4 AMR AF: 0.266

Gnomad4 ASJ AF: 0.205

Gnomad4 EAS AF: 0.479

Gnomad4 SAS AF: 0.364

Gnomad4 FIN AF: 0.276

Gnomad4 NFE AF: 0.202

Gnomad4 OTH AF: 0.196

Alfa AF: 0.206 Hom.: 1695

Bravo AF: 0.201

Asia WGS AF: 0.389 AC: 1348 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.73

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4933782; hg19: chr10-83189180;