rs593742

Variant names:

• chr15-58753575-A-G
• rs593742
• ENST00000671030.1:n.213+3440A>G

Your query was ambiguous. Multiple possible variants found:

• chr15-58753575-A-G
• chr15-58753575-A-T

Variant summary

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

The ENST00000671030.1(ENSG00000286897):​n.213+3440A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.342 in 152,134 control chromosomes in the GnomAD database, including 9,743 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 0.34 (9743 hom., cov: 33)
• Consequence: ENSG00000286897 ENST00000671030.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13
• Publications: 26 publications found

Genes affected

ENSG00000286897 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.86).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000671030.1. 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
	ENSG00000286897	ENST00000671030.1		n.213+3440A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.342 AC: 52046 AN: 152016 Hom.: 9732 Cov.: 33

Gnomad AFR AF: 0.300

Gnomad AMI AF: 0.285

Gnomad AMR AF: 0.424

Gnomad ASJ AF: 0.290

Gnomad EAS AF: 0.782

Gnomad SAS AF: 0.511

Gnomad FIN AF: 0.406

Gnomad MID AF: 0.259

Gnomad NFE AF: 0.299

Gnomad OTH AF: 0.328

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

GnomAD4 genome AF: 0.342 AC: 52093 AN: 152134 Hom.: 9743 Cov.: 33 AF XY: 0.355 AC XY: 26401 AN XY: 74388

African (AFR) AF: 0.300 AC: 12443 AN: 41490

American (AMR) AF: 0.424 AC: 6480 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.290 AC: 1008 AN: 3472

East Asian (EAS) AF: 0.782 AC: 4053 AN: 5184

South Asian (SAS) AF: 0.511 AC: 2465 AN: 4822

European-Finnish (FIN) AF: 0.406 AC: 4290 AN: 10566

Middle Eastern (MID) AF: 0.262 AC: 77 AN: 294

European-Non Finnish (NFE) AF: 0.299 AC: 20324 AN: 67988

Other (OTH) AF: 0.328 AC: 694 AN: 2116

Alfa AF: 0.304 Hom.: 1771

Bravo AF: 0.345

Asia WGS AF: 0.607 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	13
DANN	Benign	0.71
PhyloP100		1.1

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: rs593742;

hg19: chr15-59045774;