rs10513494

Positions:

• chr3-156573474-A-G

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 0.106 in 152,276 control chromosomes in the GnomAD database, including 967 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 0.11 (967 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.370

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.106 AC: 16116 AN: 152158 Hom.: 956 Cov.: 32

Gnomad AFR AF: 0.0697

Gnomad AMI AF: 0.0822

Gnomad AMR AF: 0.155

Gnomad ASJ AF: 0.0910

Gnomad EAS AF: 0.162

Gnomad SAS AF: 0.190

Gnomad FIN AF: 0.0851

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.110

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.106 AC: 16140 AN: 152276 Hom.: 967 Cov.: 32 AF XY: 0.107 AC XY: 8005 AN XY: 74468

Gnomad4 AFR AF: 0.0697

Gnomad4 AMR AF: 0.155

Gnomad4 ASJ AF: 0.0910

Gnomad4 EAS AF: 0.163

Gnomad4 SAS AF: 0.190

Gnomad4 FIN AF: 0.0851

Gnomad4 NFE AF: 0.110

Gnomad4 OTH AF: 0.127

Alfa AF: 0.114 Hom.: 535

Bravo AF: 0.108

Asia WGS AF: 0.215 AC: 746 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.81
DANN	Benign	0.43

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10513494; hg19: chr3-156291263;