rs10513251

Variant names:

• chr3-144874419-G-C
• rs10513251

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 151,614 control chromosomes in the GnomAD database, including 880 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 (880 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.530
• Publications: 1 publications found

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.152 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: 0.105 AC: 15973 AN: 151494 Hom.: 878 Cov.: 32

Gnomad AFR AF: 0.155

Gnomad AMI AF: 0.0945

Gnomad AMR AF: 0.0896

Gnomad ASJ AF: 0.0688

Gnomad EAS AF: 0.0295

Gnomad SAS AF: 0.0848

Gnomad FIN AF: 0.150

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0820

Gnomad OTH AF: 0.0879

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

GnomAD4 genome AF: 0.106 AC: 15998 AN: 151614 Hom.: 880 Cov.: 32 AF XY: 0.107 AC XY: 7950 AN XY: 74110

African (AFR) AF: 0.155 AC: 6414 AN: 41454

American (AMR) AF: 0.0896 AC: 1362 AN: 15194

Ashkenazi Jewish (ASJ) AF: 0.0688 AC: 238 AN: 3458

East Asian (EAS) AF: 0.0293 AC: 152 AN: 5184

South Asian (SAS) AF: 0.0853 AC: 411 AN: 4818

European-Finnish (FIN) AF: 0.150 AC: 1584 AN: 10572

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0820 AC: 5548 AN: 67626

Other (OTH) AF: 0.0870 AC: 183 AN: 2104

Alfa AF: 0.0963 Hom.: 91

Bravo AF: 0.102

Asia WGS AF: 0.0550 AC: 191 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.0
DANN	Benign	0.70
PhyloP100		0.53

Splicing

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

Other links and lift over

dbSNP: rs10513251; hg19: chr3-144593261;