13-42713091-C-T

Variant names:

• chr13-42713091-C-T
• rs9525667
• ENST00000799325.1:n.506+7460G>A

Variant summary

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

The ENST00000799325.1(ENSG00000304062):​n.506+7460G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.391 in 151,650 control chromosomes in the GnomAD database, including 12,241 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 0.39 (12241 hom., cov: 32)
• Consequence: ENSG00000304062 ENST00000799325.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.692
• Publications: 3 publications found

Genes affected

ENSG00000304062 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.578 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000799325.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000304062	ENST00000799325.1		n.506+7460G>A		intron	N/A
	ENSG00000304076	ENST00000799486.1		n.161+18709C>T		intron	N/A
	ENSG00000304062	ENST00000799326.1		n.*82G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.391 AC: 59238 AN: 151530 Hom.: 12234 Cov.: 32

Gnomad AFR AF: 0.238

Gnomad AMI AF: 0.424

Gnomad AMR AF: 0.446

Gnomad ASJ AF: 0.433

Gnomad EAS AF: 0.420

Gnomad SAS AF: 0.595

Gnomad FIN AF: 0.381

Gnomad MID AF: 0.427

Gnomad NFE AF: 0.452

Gnomad OTH AF: 0.434

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

GnomAD4 genome AF: 0.391 AC: 59260 AN: 151650 Hom.: 12241 Cov.: 32 AF XY: 0.393 AC XY: 29085 AN XY: 74046

African (AFR) AF: 0.238 AC: 9816 AN: 41292

American (AMR) AF: 0.446 AC: 6801 AN: 15240

Ashkenazi Jewish (ASJ) AF: 0.433 AC: 1500 AN: 3464

East Asian (EAS) AF: 0.420 AC: 2161 AN: 5150

South Asian (SAS) AF: 0.596 AC: 2869 AN: 4816

European-Finnish (FIN) AF: 0.381 AC: 3979 AN: 10444

Middle Eastern (MID) AF: 0.422 AC: 124 AN: 294

European-Non Finnish (NFE) AF: 0.452 AC: 30713 AN: 67936

Other (OTH) AF: 0.433 AC: 911 AN: 2104

Alfa AF: 0.325 Hom.: 1322

Bravo AF: 0.387

Asia WGS AF: 0.475 AC: 1650 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.4
DANN	Benign	0.61
PhyloP100		-0.69

Splicing

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

Other links and lift over

dbSNP: rs9525667; hg19: chr13-43287227;