chr7-15718375-A-T

Variant names:

• chr7-15718375-A-T
• rs2159222
• ENST00000812559.1:n.616A>T

Variant summary

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

The ENST00000812559.1(LINC02587):​n.616A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.137 in 152,160 control chromosomes in the GnomAD database, including 1,961 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 0.14 (1961 hom., cov: 32)
• Consequence: LINC02587 ENST00000812559.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.545
• Publications: 1 publications found

Genes affected

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

ENSG00000286376 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.344 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000812559.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

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

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02587	ENST00000812559.1		n.616A>T		non_coding_transcript_exon	Exon 4 of 4
	ENSG00000286376	ENST00000812475.1		n.396-1546T>A		intron	N/A
	LINC02587	ENST00000812558.1		n.1070+565A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.137 AC: 20781 AN: 152042 Hom.: 1963 Cov.: 32

Gnomad AFR AF: 0.0339

Gnomad AMI AF: 0.0833

Gnomad AMR AF: 0.222

Gnomad ASJ AF: 0.0766

Gnomad EAS AF: 0.357

Gnomad SAS AF: 0.173

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.0633

Gnomad NFE AF: 0.155

Gnomad OTH AF: 0.135

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

GnomAD4 genome AF: 0.137 AC: 20787 AN: 152160 Hom.: 1961 Cov.: 32 AF XY: 0.141 AC XY: 10500 AN XY: 74392

African (AFR) AF: 0.0338 AC: 1404 AN: 41566

American (AMR) AF: 0.222 AC: 3380 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0766 AC: 266 AN: 3472

East Asian (EAS) AF: 0.357 AC: 1846 AN: 5168

South Asian (SAS) AF: 0.173 AC: 833 AN: 4822

European-Finnish (FIN) AF: 0.202 AC: 2133 AN: 10584

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.155 AC: 10542 AN: 67972

Other (OTH) AF: 0.136 AC: 287 AN: 2114

Alfa AF: 0.143 Hom.: 245

Bravo AF: 0.134

Asia WGS AF: 0.215 AC: 747 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.7
DANN	Benign	0.60
PhyloP100		0.55

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2159222;

hg19: chr7-15758000;