rs1410425

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 1 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=-0.81).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.337 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.933+14589G>A		intron	N/A

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

African (AFR) AF: 0.0328 AC: 1364 AN: 41558

American (AMR) AF: 0.102 AC: 1554 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.0613 AC: 213 AN: 3472

East Asian (EAS) AF: 0.350 AC: 1814 AN: 5180

South Asian (SAS) AF: 0.109 AC: 525 AN: 4816

European-Finnish (FIN) AF: 0.0733 AC: 777 AN: 10594

Middle Eastern (MID) AF: 0.0306 AC: 9 AN: 294

European-Non Finnish (NFE) AF: 0.0341 AC: 2321 AN: 68030

Other (OTH) AF: 0.0620 AC: 131 AN: 2112

Alfa AF: 0.0485 Hom.: 596

Bravo AF: 0.0616

Asia WGS AF: 0.207 AC: 719 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	12
DANN	Benign	0.59
PhyloP100		0.66

Splicing

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

Other links and lift over

dbSNP: rs1410425; hg19: chr13-110198159;