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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000650264.1. 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
	ENSG00000285534	ENST00000650264.1		n.759-27823T>C		intron	N/A
	ENSG00000296995	ENST00000744136.1		n.*94A>G		downstream_gene	N/A
	ENSG00000296995	ENST00000744137.1		n.*94A>G		downstream_gene	N/A

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 v4.9

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;