rs10513430

Variant names:

• chr3-152640612-A-T
• rs10513430

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 0.0825 in 152,068 control chromosomes in the GnomAD database, including 1,150 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 0.083 (1150 hom., cov: 31)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0180
• Publications: 0 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.22 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: 0.0824 AC: 12520 AN: 151950 Hom.: 1144 Cov.: 31

Gnomad AFR AF: 0.224

Gnomad AMI AF: 0.0154

Gnomad AMR AF: 0.0475

Gnomad ASJ AF: 0.0173

Gnomad EAS AF: 0.161

Gnomad SAS AF: 0.0164

Gnomad FIN AF: 0.00349

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0202

Gnomad OTH AF: 0.0703

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

GnomAD4 genome AF: 0.0825 AC: 12546 AN: 152068 Hom.: 1150 Cov.: 31 AF XY: 0.0805 AC XY: 5986 AN XY: 74352

African (AFR) AF: 0.224 AC: 9274 AN: 41408

American (AMR) AF: 0.0474 AC: 723 AN: 15252

Ashkenazi Jewish (ASJ) AF: 0.0173 AC: 60 AN: 3468

East Asian (EAS) AF: 0.161 AC: 836 AN: 5178

South Asian (SAS) AF: 0.0160 AC: 77 AN: 4826

European-Finnish (FIN) AF: 0.00349 AC: 37 AN: 10602

Middle Eastern (MID) AF: 0.0170 AC: 5 AN: 294

European-Non Finnish (NFE) AF: 0.0202 AC: 1374 AN: 68018

Other (OTH) AF: 0.0691 AC: 146 AN: 2112

Alfa AF: 0.0538 Hom.: 81

Bravo AF: 0.0929

Asia WGS AF: 0.106 AC: 368 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	6.7
DANN	Benign	0.72
PhyloP100		-0.018

Splicing

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

Other links and lift over

dbSNP: rs10513430; hg19: chr3-152358401;