rs4462453

Variant names:

• chr13-109598981-A-G
• rs4462453
• ENST00000650264.1:n.759-27823T>C

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-27823T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.326 in 150,942 control chromosomes in the GnomAD database, including 9,559 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 0.33 (9559 hom., cov: 33)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.320
• Publications: 2 publications found

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.542 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC124903210	XR_007063870.1	n.941-6633T>C		intron_variant	Intron 1 of 1
LOC101927627	XR_007063867.1	n.*239A>G		downstream_gene_variant
LOC101927627	XR_007063868.1	n.*239A>G		downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000285534	ENST00000650264.1	n.759-27823T>C		intron_variant	Intron 1 of 3
ENSG00000296995	ENST00000744136.1	n.*94A>G		downstream_gene_variant
ENSG00000296995	ENST00000744137.1	n.*94A>G		downstream_gene_variant

Frequencies

GnomAD3 genomes AF: 0.325 AC: 49071 AN: 150824 Hom.: 9518 Cov.: 33

Gnomad AFR AF: 0.548

Gnomad AMI AF: 0.252

Gnomad AMR AF: 0.244

Gnomad ASJ AF: 0.272

Gnomad EAS AF: 0.0950

Gnomad SAS AF: 0.210

Gnomad FIN AF: 0.220

Gnomad MID AF: 0.207

Gnomad NFE AF: 0.255

Gnomad OTH AF: 0.297

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

GnomAD4 genome AF: 0.326 AC: 49169 AN: 150942 Hom.: 9559 Cov.: 33 AF XY: 0.319 AC XY: 23566 AN XY: 73778

African (AFR) AF: 0.548 AC: 22707 AN: 41436

American (AMR) AF: 0.244 AC: 3711 AN: 15180

Ashkenazi Jewish (ASJ) AF: 0.272 AC: 890 AN: 3278

East Asian (EAS) AF: 0.0961 AC: 499 AN: 5190

South Asian (SAS) AF: 0.210 AC: 1013 AN: 4816

European-Finnish (FIN) AF: 0.220 AC: 2316 AN: 10520

Middle Eastern (MID) AF: 0.205 AC: 60 AN: 292

European-Non Finnish (NFE) AF: 0.255 AC: 17128 AN: 67226

Other (OTH) AF: 0.294 AC: 617 AN: 2098

Alfa AF: 0.295 Hom.: 1948

Bravo AF: 0.331

Asia WGS AF: 0.165 AC: 577 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.1
DANN	Benign	0.39
PhyloP100		-0.32

Splicing

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

Other links and lift over

dbSNP: rs4462453; hg19: chr13-110251328;