rs10513598

Variant names:

• chr3-162986232-G-A
• rs10513598
• ENST00000796986.1:n.279-591C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-162986232-G-A
• chr3-162986232-G-C
• chr3-162986232-G-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000796986.1(ENSG00000303757):​n.279-591C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0998 in 152,106 control chromosomes in the GnomAD database, including 792 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 0.10 (792 hom., cov: 32)
• Consequence: ENSG00000303757 ENST00000796986.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.229
• Publications: 2 publications found

Genes affected

ENSG00000303757 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.105 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
ENSG00000303757	ENST00000796986.1	n.279-591C>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.100 AC: 15193 AN: 151988 Hom.: 792 Cov.: 32

Gnomad AFR AF: 0.0988

Gnomad AMI AF: 0.0493

Gnomad AMR AF: 0.101

Gnomad ASJ AF: 0.0939

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.0800

Gnomad FIN AF: 0.116

Gnomad MID AF: 0.120

Gnomad NFE AF: 0.107

Gnomad OTH AF: 0.122

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

GnomAD4 genome AF: 0.0998 AC: 15186 AN: 152106 Hom.: 792 Cov.: 32 AF XY: 0.0982 AC XY: 7303 AN XY: 74342

African (AFR) AF: 0.0985 AC: 4087 AN: 41508

American (AMR) AF: 0.101 AC: 1538 AN: 15272

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

East Asian (EAS) AF: 0.00 AC: 0 AN: 5156

South Asian (SAS) AF: 0.0792 AC: 381 AN: 4810

European-Finnish (FIN) AF: 0.116 AC: 1232 AN: 10598

Middle Eastern (MID) AF: 0.129 AC: 38 AN: 294

European-Non Finnish (NFE) AF: 0.107 AC: 7285 AN: 67980

Other (OTH) AF: 0.121 AC: 254 AN: 2106

Alfa AF: 0.102 Hom.: 860

Bravo AF: 0.0980

Asia WGS AF: 0.0470 AC: 163 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	5.6
DANN	Benign	0.51
PhyloP100		0.23

Splicing

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

Other links and lift over

dbSNP: rs10513598; hg19: chr3-162704020;