rs10513442

Variant names:

• chr3-153273601-A-T
• rs10513442
• ENST00000757134.1:n.618+21815A>T

Variant summary

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

The ENST00000757134.1(ENSG00000289885):​n.618+21815A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0384 in 152,302 control chromosomes in the GnomAD database, including 154 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 0.038 (154 hom., cov: 32)
• Consequence: ENSG00000289885 ENST00000757134.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.918
• Publications: 1 publications found

Genes affected

ENSG00000289885 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0589 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000757134.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000289885	ENST00000757134.1		n.618+21815A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0384 AC: 5841 AN: 152184 Hom.: 154 Cov.: 32

Gnomad AFR AF: 0.0114

Gnomad AMI AF: 0.108

Gnomad AMR AF: 0.0365

Gnomad ASJ AF: 0.0645

Gnomad EAS AF: 0.00636

Gnomad SAS AF: 0.0311

Gnomad FIN AF: 0.00895

Gnomad MID AF: 0.0411

Gnomad NFE AF: 0.0605

Gnomad OTH AF: 0.0382

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

GnomAD4 genome AF: 0.0384 AC: 5841 AN: 152302 Hom.: 154 Cov.: 32 AF XY: 0.0362 AC XY: 2697 AN XY: 74480

African (AFR) AF: 0.0114 AC: 473 AN: 41574

American (AMR) AF: 0.0365 AC: 558 AN: 15306

Ashkenazi Jewish (ASJ) AF: 0.0645 AC: 224 AN: 3472

East Asian (EAS) AF: 0.00638 AC: 33 AN: 5174

South Asian (SAS) AF: 0.0321 AC: 155 AN: 4826

European-Finnish (FIN) AF: 0.00895 AC: 95 AN: 10618

Middle Eastern (MID) AF: 0.0374 AC: 11 AN: 294

European-Non Finnish (NFE) AF: 0.0605 AC: 4114 AN: 68012

Other (OTH) AF: 0.0378 AC: 80 AN: 2116

Alfa AF: 0.0455 Hom.: 19

Bravo AF: 0.0388

Asia WGS AF: 0.0200 AC: 70 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.68
DANN	Benign	0.75
PhyloP100		-0.92

Splicing

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

Other links and lift over

dbSNP: rs10513442; hg19: chr3-152991390;