7-15695090-T-G

Variant names:

• chr7-15695090-T-G
• rs726395
• ENST00000442176.3:n.487T>G

Variant summary

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

The ENST00000442176.3(LINC02587):​n.487T>G 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 0.503 in 152,078 control chromosomes in the GnomAD database, including 19,743 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 0.50 (19742 hom., cov: 33)
  • Exomes 𝑓: 0.75 (1 hom.)
• Consequence: LINC02587 ENST00000442176.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.516
• Publications: 6 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.582 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02587	NR_110094.1	n.296T>G		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02587	ENST00000442176.3	n.487T>G		non_coding_transcript_exon_variant	Exon 2 of 2	3
LINC02587	ENST00000663069.4	n.278T>G		non_coding_transcript_exon_variant	Exon 2 of 3
LINC02587	ENST00000812558.1	n.488T>G		non_coding_transcript_exon_variant	Exon 2 of 6

Frequencies

GnomAD3 genomes AF: 0.503 AC: 76493 AN: 151956 Hom.: 19734 Cov.: 33

Gnomad AFR AF: 0.416

Gnomad AMI AF: 0.529

Gnomad AMR AF: 0.504

Gnomad ASJ AF: 0.652

Gnomad EAS AF: 0.508

Gnomad SAS AF: 0.601

Gnomad FIN AF: 0.499

Gnomad MID AF: 0.538

Gnomad NFE AF: 0.542

Gnomad OTH AF: 0.511

GnomAD4 exome AF: 0.750 AC: 3 AN: 4 Hom.: 1 Cov.: 0 AF XY: 1.00 AC XY: 2 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.750 AC: 3 AN: 4

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.503 AC: 76547 AN: 152074 Hom.: 19742 Cov.: 33 AF XY: 0.505 AC XY: 37507 AN XY: 74330

African (AFR) AF: 0.416 AC: 17256 AN: 41484

American (AMR) AF: 0.505 AC: 7713 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.652 AC: 2263 AN: 3470

East Asian (EAS) AF: 0.507 AC: 2620 AN: 5166

South Asian (SAS) AF: 0.601 AC: 2892 AN: 4814

European-Finnish (FIN) AF: 0.499 AC: 5267 AN: 10556

Middle Eastern (MID) AF: 0.541 AC: 158 AN: 292

European-Non Finnish (NFE) AF: 0.542 AC: 36817 AN: 67980

Other (OTH) AF: 0.510 AC: 1079 AN: 2114

Alfa AF: 0.532 Hom.: 94896

Bravo AF: 0.501

Asia WGS AF: 0.576 AC: 2001 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	9.8
DANN	Benign	0.79
PhyloP100		0.52

Splicing

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

Other links and lift over

dbSNP: rs726395; hg19: chr7-15734715;