chr3-156573474-A-G

Variant names:

• chr3-156573474-A-G
• rs10513494

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 0.106 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
• Publications: 5 publications found

ACMG classification

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	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

African (AFR) AF: 0.0697 AC: 2897 AN: 41544

American (AMR) AF: 0.155 AC: 2370 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.0910 AC: 316 AN: 3472

East Asian (EAS) AF: 0.163 AC: 846 AN: 5192

South Asian (SAS) AF: 0.190 AC: 917 AN: 4828

European-Finnish (FIN) AF: 0.0851 AC: 904 AN: 10622

Middle Eastern (MID) AF: 0.136 AC: 40 AN: 294

European-Non Finnish (NFE) AF: 0.110 AC: 7507 AN: 68012

Other (OTH) AF: 0.127 AC: 268 AN: 2114

Alfa AF: 0.114 Hom.: 584

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
PhyloP100		-0.37

Splicing

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

Other links and lift over

dbSNP: rs10513494; hg19: chr3-156291263;