rs10029539

Variant names:

• chr4-31790330-T-C
• rs10029539

Variant summary

Our verdict is Benign. Variant got -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

ACMG classification

Verdict is Benign. Variant got -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.

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: 0.431 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

Gnomad4 AFR AF: 0.234

Gnomad4 AMR AF: 0.441

Gnomad4 ASJ AF: 0.469

Gnomad4 EAS AF: 0.621

Gnomad4 SAS AF: 0.447

Gnomad4 FIN AF: 0.479

Gnomad4 NFE AF: 0.525

Gnomad4 OTH AF: 0.447

Alfa AF: 0.502 Hom.: 15041

Bravo AF: 0.420

Asia WGS AF: 0.484 AC: 1677 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10029539; hg19: chr4-31791952;