13-74707684-A-G

Variant names:

• chr13-74707684-A-G
• rs2104615
• ENST00000814867.1:n.124+25016T>C

Variant summary

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

The ENST00000814867.1(ENSG00000306024):​n.124+25016T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.439 in 152,114 control chromosomes in the GnomAD database, including 14,828 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 0.44 (14828 hom., cov: 33)
• Consequence: ENSG00000306024 ENST00000814867.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.540
• Publications: 4 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 = 0.577 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000814867.1. 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000306024	ENST00000814867.1		n.124+25016T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.439 AC: 66751 AN: 151996 Hom.: 14828 Cov.: 33

Gnomad AFR AF: 0.399

Gnomad AMI AF: 0.422

Gnomad AMR AF: 0.477

Gnomad ASJ AF: 0.490

Gnomad EAS AF: 0.595

Gnomad SAS AF: 0.537

Gnomad FIN AF: 0.505

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.423

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.439 AC: 66767 AN: 152114 Hom.: 14828 Cov.: 33 AF XY: 0.444 AC XY: 32974 AN XY: 74348

African (AFR) AF: 0.398 AC: 16513 AN: 41486

American (AMR) AF: 0.477 AC: 7297 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.490 AC: 1699 AN: 3470

East Asian (EAS) AF: 0.594 AC: 3075 AN: 5174

South Asian (SAS) AF: 0.537 AC: 2592 AN: 4830

European-Finnish (FIN) AF: 0.505 AC: 5328 AN: 10556

Middle Eastern (MID) AF: 0.473 AC: 139 AN: 294

European-Non Finnish (NFE) AF: 0.423 AC: 28758 AN: 67986

Other (OTH) AF: 0.464 AC: 981 AN: 2114

Alfa AF: 0.429 Hom.: 26549

Bravo AF: 0.440

Asia WGS AF: 0.557 AC: 1938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	4.2
DANN	Benign	0.77
PhyloP100		0.54

Splicing

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

Other links and lift over

dbSNP: rs2104615; hg19: chr13-75281821;