rs4933782

Variant names:

• chr10-81429424-C-T
• rs4933782

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 0.204 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
• Publications: 2 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.463 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: 0.204 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

African (AFR) AF: 0.112 AC: 4609 AN: 41290

American (AMR) AF: 0.266 AC: 4050 AN: 15210

Ashkenazi Jewish (ASJ) AF: 0.205 AC: 710 AN: 3464

East Asian (EAS) AF: 0.479 AC: 2469 AN: 5152

South Asian (SAS) AF: 0.364 AC: 1746 AN: 4796

European-Finnish (FIN) AF: 0.276 AC: 2894 AN: 10486

Middle Eastern (MID) AF: 0.179 AC: 52 AN: 290

European-Non Finnish (NFE) AF: 0.202 AC: 13713 AN: 67868

Other (OTH) AF: 0.196 AC: 412 AN: 2100

Alfa AF: 0.207 Hom.: 1886

Bravo AF: 0.201

Asia WGS AF: 0.389 AC: 1348 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.41
DANN	Benign	0.73
PhyloP100		-0.77

Splicing

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

Other links and lift over

dbSNP: rs4933782; hg19: chr10-83189180;