rs10029539

Variant names:

• chr4-31790330-T-C
• rs10029539

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The variant allele was found at a frequency of 0.431 in 151,908 control chromosomes in the GnomAD database, including 15,555 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 0.43 (15555 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.92
• Publications: 2 publications found

ACMG classification

Our verdict: Benign. The variant received -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.39).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.603 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: 0.431 AC: 65424 AN: 151794 Hom.: 15546 Cov.: 32

Gnomad AFR AF: 0.234

Gnomad AMI AF: 0.284

Gnomad AMR AF: 0.441

Gnomad ASJ AF: 0.469

Gnomad EAS AF: 0.620

Gnomad SAS AF: 0.447

Gnomad FIN AF: 0.479

Gnomad MID AF: 0.443

Gnomad NFE AF: 0.525

Gnomad OTH AF: 0.443

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

GnomAD4 genome AF: 0.431 AC: 65460 AN: 151908 Hom.: 15555 Cov.: 32 AF XY: 0.432 AC XY: 32027 AN XY: 74212

African (AFR) AF: 0.234 AC: 9699 AN: 41468

American (AMR) AF: 0.441 AC: 6726 AN: 15244

Ashkenazi Jewish (ASJ) AF: 0.469 AC: 1626 AN: 3464

East Asian (EAS) AF: 0.621 AC: 3186 AN: 5134

South Asian (SAS) AF: 0.447 AC: 2153 AN: 4816

European-Finnish (FIN) AF: 0.479 AC: 5045 AN: 10540

Middle Eastern (MID) AF: 0.449 AC: 132 AN: 294

European-Non Finnish (NFE) AF: 0.525 AC: 35692 AN: 67928

Other (OTH) AF: 0.447 AC: 943 AN: 2110

Alfa AF: 0.496 Hom.: 20504

Bravo AF: 0.420

Asia WGS AF: 0.484 AC: 1677 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.39
CADD	Benign	13
DANN	Benign	0.60
PhyloP100		1.9

Splicing

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

Other links and lift over

dbSNP: rs10029539; hg19: chr4-31791952;