rs2159222

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC101927558	XR_001745101.2	n.859+565A>T		intron_variant	Intron 2 of 2
LOC101927558	XR_927057.3	n.854+565A>T		intron_variant	Intron 3 of 3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02587	ENST00000812559.1	n.616A>T		non_coding_transcript_exon_variant	Exon 4 of 4
ENSG00000286376	ENST00000812475.1	n.396-1546T>A		intron_variant	Intron 3 of 3
LINC02587	ENST00000812558.1	n.1070+565A>T		intron_variant	Intron 5 of 5

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 v4.3

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

Other links and lift over

dbSNP: rs2159222; hg19: chr7-15758000;