rs580839

Variant names:

• chr15-34706628-G-A
• rs580839
• ENST00000720751.1:n.234+13689C>T

Variant summary

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

The ENST00000720751.1(ENSG00000294065):​n.234+13689C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.499 in 151,958 control chromosomes in the GnomAD database, including 19,992 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 0.50 (19992 hom., cov: 32)
• Consequence: ENSG00000294065 ENST00000720751.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0140
• Publications: 15 publications found

Genes affected

ENSG00000294065 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000720751.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000294065	ENST00000720751.1		n.234+13689C>T		intron	N/A
	ENSG00000294065	ENST00000720752.1		n.188-3086C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.499 AC: 75696 AN: 151840 Hom.: 19955 Cov.: 32

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.654

Gnomad AMR AF: 0.410

Gnomad ASJ AF: 0.385

Gnomad EAS AF: 0.437

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.349

Gnomad MID AF: 0.335

Gnomad NFE AF: 0.433

Gnomad OTH AF: 0.467

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

GnomAD4 genome AF: 0.499 AC: 75789 AN: 151958 Hom.: 19992 Cov.: 32 AF XY: 0.493 AC XY: 36627 AN XY: 74252

African (AFR) AF: 0.683 AC: 28323 AN: 41440

American (AMR) AF: 0.409 AC: 6246 AN: 15266

Ashkenazi Jewish (ASJ) AF: 0.385 AC: 1337 AN: 3470

East Asian (EAS) AF: 0.437 AC: 2260 AN: 5174

South Asian (SAS) AF: 0.589 AC: 2830 AN: 4802

European-Finnish (FIN) AF: 0.349 AC: 3683 AN: 10552

Middle Eastern (MID) AF: 0.337 AC: 99 AN: 294

European-Non Finnish (NFE) AF: 0.433 AC: 29428 AN: 67938

Other (OTH) AF: 0.468 AC: 987 AN: 2110

Alfa AF: 0.461 Hom.: 3364

Bravo AF: 0.507

Asia WGS AF: 0.543 AC: 1890 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	1.6
DANN	Benign	0.71
PhyloP100		-0.014

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs580839;

hg19: chr15-34998829;