15-74373281-C-T

Variant names:

• chr15-74373281-C-T
• rs4077582
• ENST00000783573.1:n.116-3203G>A

Variant summary

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

The ENST00000783573.1(ENSG00000302041):​n.116-3203G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.621 in 152,112 control chromosomes in the GnomAD database, including 29,906 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 0.62 (29906 hom., cov: 32)
• Consequence: ENSG00000302041 ENST00000783573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.769
• Publications: 15 publications found

Genes affected

ENSG00000302041 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.693 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
ENSG00000302041	ENST00000783573.1	n.116-3203G>A		intron_variant	Intron 1 of 1
ENSG00000302041	ENST00000783574.1	n.186+2065G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.622 AC: 94480 AN: 151994 Hom.: 29904 Cov.: 32

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.515

Gnomad AMR AF: 0.631

Gnomad ASJ AF: 0.647

Gnomad EAS AF: 0.434

Gnomad SAS AF: 0.492

Gnomad FIN AF: 0.715

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.610

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

GnomAD4 genome AF: 0.621 AC: 94513 AN: 152112 Hom.: 29906 Cov.: 32 AF XY: 0.618 AC XY: 45916 AN XY: 74352

African (AFR) AF: 0.508 AC: 21052 AN: 41474

American (AMR) AF: 0.631 AC: 9653 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.647 AC: 2248 AN: 3472

East Asian (EAS) AF: 0.435 AC: 2247 AN: 5170

South Asian (SAS) AF: 0.491 AC: 2368 AN: 4818

European-Finnish (FIN) AF: 0.715 AC: 7567 AN: 10590

Middle Eastern (MID) AF: 0.626 AC: 184 AN: 294

European-Non Finnish (NFE) AF: 0.698 AC: 47447 AN: 67974

Other (OTH) AF: 0.605 AC: 1278 AN: 2114

Alfa AF: 0.647 Hom.: 9224

Bravo AF: 0.612

Asia WGS AF: 0.438 AC: 1523 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	7.0
DANN	Benign	0.58
PhyloP100		0.77

Splicing

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

Other links and lift over

dbSNP: rs4077582; hg19: chr15-74665622;