chr7-15703161-G-A

Variant names:

• chr7-15703161-G-A
• rs10486776
• ENST00000812558.1:n.920+6777G>A

Variant summary

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

The ENST00000812558.1(LINC02587):​n.920+6777G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0621 in 152,170 control chromosomes in the GnomAD database, including 423 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 0.062 (423 hom., cov: 32)
• Consequence: LINC02587 ENST00000812558.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.689
• Publications: 12 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.132 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

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02587	ENST00000812558.1		n.920+6777G>A		intron	N/A
	LINC02587	ENST00000812559.1		n.39-12364G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0621 AC: 9450 AN: 152052 Hom.: 424 Cov.: 32

Gnomad AFR AF: 0.0175

Gnomad AMI AF: 0.0724

Gnomad AMR AF: 0.0809

Gnomad ASJ AF: 0.0651

Gnomad EAS AF: 0.141

Gnomad SAS AF: 0.133

Gnomad FIN AF: 0.0588

Gnomad MID AF: 0.185

Gnomad NFE AF: 0.0730

Gnomad OTH AF: 0.0877

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

GnomAD4 genome AF: 0.0621 AC: 9448 AN: 152170 Hom.: 423 Cov.: 32 AF XY: 0.0630 AC XY: 4685 AN XY: 74380

African (AFR) AF: 0.0175 AC: 725 AN: 41536

American (AMR) AF: 0.0811 AC: 1239 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0651 AC: 226 AN: 3472

East Asian (EAS) AF: 0.141 AC: 729 AN: 5172

South Asian (SAS) AF: 0.133 AC: 642 AN: 4822

European-Finnish (FIN) AF: 0.0588 AC: 623 AN: 10592

Middle Eastern (MID) AF: 0.178 AC: 52 AN: 292

European-Non Finnish (NFE) AF: 0.0729 AC: 4959 AN: 67994

Other (OTH) AF: 0.0887 AC: 187 AN: 2108

Alfa AF: 0.0723 Hom.: 690

Bravo AF: 0.0625

Asia WGS AF: 0.123 AC: 429 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	7.9
DANN	Benign	0.66
PhyloP100		0.69

Splicing

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

Other links and lift over

dbSNP: rs10486776; hg19: chr7-15742786;