ENST00000650264.1:n.759-61973A>G

Variant names:

• chr13-109633131-T-C
• rs1929210
• ENST00000650264.1:n.759-61973A>G

Variant summary

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

The ENST00000650264.1(ENSG00000285534):​n.759-61973A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.493 in 151,760 control chromosomes in the GnomAD database, including 18,685 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 0.49 (18685 hom., cov: 30)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.268
• Publications: 4 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 (EAS) allele frequency at 95% confidence interval = 0.618 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
ENSG00000285534	ENST00000650264.1	n.759-61973A>G		intron_variant	Intron 1 of 3

Frequencies

GnomAD3 genomes AF: 0.492 AC: 74679 AN: 151642 Hom.: 18662 Cov.: 30

Gnomad AFR AF: 0.522

Gnomad AMI AF: 0.355

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.439

Gnomad EAS AF: 0.636

Gnomad SAS AF: 0.614

Gnomad FIN AF: 0.455

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.442

Gnomad OTH AF: 0.487

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

GnomAD4 genome AF: 0.493 AC: 74747 AN: 151760 Hom.: 18685 Cov.: 30 AF XY: 0.501 AC XY: 37136 AN XY: 74142

African (AFR) AF: 0.522 AC: 21592 AN: 41348

American (AMR) AF: 0.597 AC: 9110 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.439 AC: 1524 AN: 3468

East Asian (EAS) AF: 0.636 AC: 3256 AN: 5116

South Asian (SAS) AF: 0.615 AC: 2959 AN: 4808

European-Finnish (FIN) AF: 0.455 AC: 4787 AN: 10514

Middle Eastern (MID) AF: 0.480 AC: 141 AN: 294

European-Non Finnish (NFE) AF: 0.442 AC: 30033 AN: 67938

Other (OTH) AF: 0.487 AC: 1023 AN: 2102

Alfa AF: 0.467 Hom.: 34245

Bravo AF: 0.502

Asia WGS AF: 0.572 AC: 1990 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	5.5
DANN	Benign	0.88
PhyloP100		0.27

Splicing

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

Other links and lift over

dbSNP: rs1929210; hg19: chr13-110285478;