rs593742

Positions:

• 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, non coding transcript 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: ENST00000671030.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.13

Genes affected

(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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
	ENST00000671030.1	n.213+3440A>G		intron_variant, non_coding_transcript_variant

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;