rs4077581

Variant names:

• chr15-74373173-C-T
• rs4077581
• ENST00000783573.1:n.116-3095G>A

Variant summary

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

The ENST00000783573.1(ENSG00000302041):​n.116-3095G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.623 in 152,042 control chromosomes in the GnomAD database, including 30,015 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 (30015 hom., cov: 33)
• Consequence: ENSG00000302041 ENST00000783573.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590
• Publications: 3 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=-0.72).
• 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.116-3095G>A		intron_variant	Intron 1 of 1
ENSG00000302041	ENST00000783574.1	n.186+2173G>A		intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes AF: 0.623 AC: 94679 AN: 151924 Hom.: 30013 Cov.: 33

Gnomad AFR AF: 0.514

Gnomad AMI AF: 0.514

Gnomad AMR AF: 0.632

Gnomad ASJ AF: 0.648

Gnomad EAS AF: 0.433

Gnomad SAS AF: 0.491

Gnomad FIN AF: 0.714

Gnomad MID AF: 0.633

Gnomad NFE AF: 0.698

Gnomad OTH AF: 0.611

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

GnomAD4 genome AF: 0.623 AC: 94715 AN: 152042 Hom.: 30015 Cov.: 33 AF XY: 0.619 AC XY: 45998 AN XY: 74300

African (AFR) AF: 0.514 AC: 21287 AN: 41440

American (AMR) AF: 0.632 AC: 9655 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.648 AC: 2247 AN: 3470

East Asian (EAS) AF: 0.434 AC: 2247 AN: 5174

South Asian (SAS) AF: 0.491 AC: 2367 AN: 4820

European-Finnish (FIN) AF: 0.714 AC: 7530 AN: 10550

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

European-Non Finnish (NFE) AF: 0.698 AC: 47451 AN: 67990

Other (OTH) AF: 0.606 AC: 1279 AN: 2112

Alfa AF: 0.662 Hom.: 4940

Bravo AF: 0.614

Asia WGS AF: 0.441 AC: 1532 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.72
CADD	Benign	3.6
DANN	Benign	0.84
PhyloP100		-0.59

Splicing

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

Other links and lift over

dbSNP: rs4077581; hg19: chr15-74665514;