15-38867389-C-T

Position:

• chr15-38867389-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000560197.5(ENSG00000259345):​n.977+581G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.646 in 151,986 control chromosomes in the GnomAD database, including 32,848 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 0.65 (32848 hom., cov: 31)
• Consequence: ENSG00000259345 ENST00000560197.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.00

Genes affected

ENSG00000259345 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LOC105370777	XR_001751487.2	n.287+581G>A		intron_variant
LOC105370777	XR_932130.3	n.244+581G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000259345	ENST00000560197.5	n.977+581G>A		intron_variant		5
LINC02694	ENST00000644461.1	n.158+44330C>T		intron_variant
LINC02694	ENST00000646232.1	n.225+44330C>T		intron_variant
LINC02694	ENST00000647456.1	n.659-123896C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.645 AC: 97993 AN: 151868 Hom.: 32796 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.336

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.598

Gnomad EAS AF: 0.922

Gnomad SAS AF: 0.669

Gnomad FIN AF: 0.478

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.557

Gnomad OTH AF: 0.646

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

GnomAD4 genome AF: 0.646 AC: 98108 AN: 151986 Hom.: 32848 Cov.: 31 AF XY: 0.645 AC XY: 47924 AN XY: 74264

Gnomad4 AFR AF: 0.783

Gnomad4 AMR AF: 0.713

Gnomad4 ASJ AF: 0.598

Gnomad4 EAS AF: 0.921

Gnomad4 SAS AF: 0.667

Gnomad4 FIN AF: 0.478

Gnomad4 NFE AF: 0.557

Gnomad4 OTH AF: 0.650

Alfa AF: 0.582 Hom.: 36270

Bravo AF: 0.672

Asia WGS AF: 0.821 AC: 2854 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.2
DANN	Benign	0.46

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2725795; hg19: chr15-39159590;