rs10512739

Variant names:

• chr5-40431779-A-G
• rs10512739

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 0.085 in 152,258 control chromosomes in the GnomAD database, including 763 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 0.085 (763 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 2.84
• Publications: 10 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.181 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: 0.0848 AC: 12907 AN: 152140 Hom.: 753 Cov.: 32

Gnomad AFR AF: 0.0478

Gnomad AMI AF: 0.201

Gnomad AMR AF: 0.186

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.118

Gnomad SAS AF: 0.0588

Gnomad FIN AF: 0.0458

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.0882

Gnomad OTH AF: 0.0861

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

GnomAD4 genome AF: 0.0850 AC: 12942 AN: 152258 Hom.: 763 Cov.: 32 AF XY: 0.0846 AC XY: 6295 AN XY: 74452

African (AFR) AF: 0.0480 AC: 1996 AN: 41550

American (AMR) AF: 0.187 AC: 2854 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.0939 AC: 326 AN: 3470

East Asian (EAS) AF: 0.118 AC: 610 AN: 5186

South Asian (SAS) AF: 0.0595 AC: 287 AN: 4826

European-Finnish (FIN) AF: 0.0458 AC: 486 AN: 10618

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0882 AC: 5997 AN: 68018

Other (OTH) AF: 0.0862 AC: 182 AN: 2112

Alfa AF: 0.0905 Hom.: 404

Bravo AF: 0.0990

Asia WGS AF: 0.0680 AC: 237 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	9.6
DANN	Benign	0.73
PhyloP100		2.8

Splicing

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

Other links and lift over

dbSNP: rs10512739; hg19: chr5-40431881;