13-109633131-T-C

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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

Gnomad4 AFR AF: 0.522

Gnomad4 AMR AF: 0.597

Gnomad4 ASJ AF: 0.439

Gnomad4 EAS AF: 0.636

Gnomad4 SAS AF: 0.615

Gnomad4 FIN AF: 0.455

Gnomad4 NFE AF: 0.442

Gnomad4 OTH AF: 0.487

Alfa AF: 0.462 Hom.: 22828

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1929210; hg19: chr13-110285478;