rs10513320

Variant names:

• chr3-147754588-G-A
• rs10513320
• ENST00000819924.1:n.473+3528C>T

Your query was ambiguous. Multiple possible variants found:

• chr3-147754588-G-A
• chr3-147754588-G-C
• chr3-147754588-G-T

Variant summary

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

The ENST00000819924.1(ENSG00000289451):​n.473+3528C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.188 in 151,922 control chromosomes in the GnomAD database, including 3,406 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 0.19 (3406 hom., cov: 32)
• Consequence: ENSG00000289451 ENST00000819924.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.587
• Publications: 4 publications found

Genes affected

ENSG00000289451 (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 (EAS) allele frequency at 95% confidence interval = 0.469 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC102724145	XR_427423.3	n.358+3528C>T		intron_variant	Intron 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000289451	ENST00000819924.1	n.473+3528C>T		intron_variant	Intron 2 of 2
ENSG00000289451	ENST00000819925.1	n.334+3528C>T		intron_variant	Intron 2 of 2
ENSG00000289451	ENST00000819927.1	n.367+3528C>T		intron_variant	Intron 2 of 2
ENSG00000289451	ENST00000819928.1	n.332+3528C>T		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.188 AC: 28597 AN: 151804 Hom.: 3400 Cov.: 32

Gnomad AFR AF: 0.0629

Gnomad AMI AF: 0.174

Gnomad AMR AF: 0.215

Gnomad ASJ AF: 0.149

Gnomad EAS AF: 0.485

Gnomad SAS AF: 0.275

Gnomad FIN AF: 0.230

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.226

Gnomad OTH AF: 0.191

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

GnomAD4 genome AF: 0.188 AC: 28609 AN: 151922 Hom.: 3406 Cov.: 32 AF XY: 0.191 AC XY: 14203 AN XY: 74238

African (AFR) AF: 0.0628 AC: 2607 AN: 41516

American (AMR) AF: 0.215 AC: 3279 AN: 15216

Ashkenazi Jewish (ASJ) AF: 0.149 AC: 516 AN: 3468

East Asian (EAS) AF: 0.485 AC: 2489 AN: 5134

South Asian (SAS) AF: 0.276 AC: 1330 AN: 4814

European-Finnish (FIN) AF: 0.230 AC: 2429 AN: 10554

Middle Eastern (MID) AF: 0.150 AC: 44 AN: 294

European-Non Finnish (NFE) AF: 0.226 AC: 15349 AN: 67910

Other (OTH) AF: 0.194 AC: 408 AN: 2106

Alfa AF: 0.208 Hom.: 10494

Bravo AF: 0.180

Asia WGS AF: 0.364 AC: 1257 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.15
DANN	Benign	0.36
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs10513320; hg19: chr3-147472375;