ENST00000812558.1:n.920+9315T>C

Variant names:

• chr7-15705699-T-C
• rs6942413
• ENST00000812558.1:n.920+9315T>C

Variant summary

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

The ENST00000812558.1(LINC02587):​n.920+9315T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.542 in 151,888 control chromosomes in the GnomAD database, including 23,176 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 0.54 (23176 hom., cov: 31)
• Consequence: LINC02587 ENST00000812558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 1 publications found

Genes affected

LINC02587 (HGNC:50672): (long intergenic non-protein coding RNA 2587)

LOC101927558 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.668 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812558.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02587	ENST00000812558.1		n.920+9315T>C		intron	N/A
	LINC02587	ENST00000812559.1		n.39-9826T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.542 AC: 82301 AN: 151770 Hom.: 23152 Cov.: 31

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.452

Gnomad AMR AF: 0.550

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.644

Gnomad SAS AF: 0.453

Gnomad FIN AF: 0.536

Gnomad MID AF: 0.548

Gnomad NFE AF: 0.469

Gnomad OTH AF: 0.549

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

GnomAD4 genome AF: 0.542 AC: 82365 AN: 151888 Hom.: 23176 Cov.: 31 AF XY: 0.543 AC XY: 40285 AN XY: 74232

African (AFR) AF: 0.675 AC: 27943 AN: 41420

American (AMR) AF: 0.550 AC: 8388 AN: 15258

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1315 AN: 3468

East Asian (EAS) AF: 0.644 AC: 3323 AN: 5158

South Asian (SAS) AF: 0.453 AC: 2177 AN: 4810

European-Finnish (FIN) AF: 0.536 AC: 5654 AN: 10550

Middle Eastern (MID) AF: 0.538 AC: 157 AN: 292

European-Non Finnish (NFE) AF: 0.469 AC: 31846 AN: 67922

Other (OTH) AF: 0.548 AC: 1152 AN: 2102

Alfa AF: 0.494 Hom.: 51674

Bravo AF: 0.548

Asia WGS AF: 0.515 AC: 1788 AN: 3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	4.5
DANN	Benign	0.77
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs6942413; hg19: chr7-15745324;