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. Variant got -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

Genes affected

ENSG00000286897 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

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
ENSG00000286897	ENST00000671030.1	n.213+3440A>G		intron_variant	Intron 1 of 1

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

Gnomad4 AFR AF: 0.300

Gnomad4 AMR AF: 0.424

Gnomad4 ASJ AF: 0.290

Gnomad4 EAS AF: 0.782

Gnomad4 SAS AF: 0.511

Gnomad4 FIN AF: 0.406

Gnomad4 NFE AF: 0.299

Gnomad4 OTH AF: 0.328

Alfa AF: 0.304 Hom.: 1742

Bravo AF: 0.345

Asia WGS AF: 0.607 AC: 2105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs593742; hg19: chr15-59045774;