rs1410425

Variant names:

• chr13-109545812-C-T
• rs1410425
• ENST00000650264.1:n.933+14589G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000650264.1(ENSG00000285534):​n.933+14589G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0579 in 152,256 control chromosomes in the GnomAD database, including 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 0.058 (559 hom., cov: 33)
• Consequence: ENSG00000285534 ENST00000650264.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.658

Genes affected

ENSG00000285534 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 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.933+14589G>A		intron_variant	Intron 3 of 3

Frequencies

GnomAD3 genomes AF: 0.0580 AC: 8818 AN: 152138 Hom.: 561 Cov.: 33

Gnomad AFR AF: 0.0329

Gnomad AMI AF: 0.111

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.0613

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.109

Gnomad FIN AF: 0.0733

Gnomad MID AF: 0.0316

Gnomad NFE AF: 0.0341

Gnomad OTH AF: 0.0627

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

GnomAD4 genome AF: 0.0579 AC: 8809 AN: 152256 Hom.: 559 Cov.: 33 AF XY: 0.0631 AC XY: 4694 AN XY: 74436

Gnomad4 AFR AF: 0.0328

Gnomad4 AMR AF: 0.102

Gnomad4 ASJ AF: 0.0613

Gnomad4 EAS AF: 0.350

Gnomad4 SAS AF: 0.109

Gnomad4 FIN AF: 0.0733

Gnomad4 NFE AF: 0.0341

Gnomad4 OTH AF: 0.0620

Alfa AF: 0.0503 Hom.: 57

Bravo AF: 0.0616

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1410425; hg19: chr13-110198159;