13-74708758-C-T

Variant names:

• chr13-74708758-C-T
• rs869878
• ENST00000814867.1:n.124+23942G>A

Variant summary

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

The ENST00000814867.1(ENSG00000306024):​n.124+23942G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,208 control chromosomes in the GnomAD database, including 43,701 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 0.75 (43701 hom., cov: 34)
• Consequence: ENSG00000306024 ENST00000814867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0470
• Publications: 10 publications found

Genes affected

ENSG00000306024 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.888 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
ENSG00000306024	ENST00000814867.1	n.124+23942G>A		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114693 AN: 152090 Hom.: 43676 Cov.: 34

Gnomad AFR AF: 0.695

Gnomad AMI AF: 0.734

Gnomad AMR AF: 0.851

Gnomad ASJ AF: 0.885

Gnomad EAS AF: 0.910

Gnomad SAS AF: 0.889

Gnomad FIN AF: 0.781

Gnomad MID AF: 0.905

Gnomad NFE AF: 0.734

Gnomad OTH AF: 0.804

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

GnomAD4 genome AF: 0.754 AC: 114770 AN: 152208 Hom.: 43701 Cov.: 34 AF XY: 0.760 AC XY: 56553 AN XY: 74410

African (AFR) AF: 0.696 AC: 28876 AN: 41516

American (AMR) AF: 0.851 AC: 13011 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.885 AC: 3071 AN: 3472

East Asian (EAS) AF: 0.910 AC: 4704 AN: 5172

South Asian (SAS) AF: 0.889 AC: 4286 AN: 4822

European-Finnish (FIN) AF: 0.781 AC: 8283 AN: 10608

Middle Eastern (MID) AF: 0.912 AC: 268 AN: 294

European-Non Finnish (NFE) AF: 0.734 AC: 49916 AN: 68014

Other (OTH) AF: 0.798 AC: 1687 AN: 2114

Alfa AF: 0.757 Hom.: 80109

Bravo AF: 0.760

Asia WGS AF: 0.857 AC: 2978 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	2.5
DANN	Benign	0.54
PhyloP100		-0.047

Splicing

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

Other links and lift over

dbSNP: rs869878; hg19: chr13-75282895;