9-102559589-G-T

Variant names:

• chr9-102559589-G-T
• rs10512300
• ENST00000374801.3:n.74-18682G>T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000374801.3(LINC00587):​n.74-18682G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.036 in 152,200 control chromosomes in the GnomAD database, including 441 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 0.036 (441 hom., cov: 32)
• Consequence: LINC00587 ENST00000374801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.383

Genes affected

LINC00587 (HGNC:31372): (long intergenic non-protein coding RNA 587)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.363 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00587	NR_103830.1	n.73-18682G>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00587	ENST00000374801.3	n.74-18682G>T		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes AF: 0.0361 AC: 5487 AN: 152082 Hom.: 442 Cov.: 32

Gnomad AFR AF: 0.00775

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0333

Gnomad ASJ AF: 0.0130

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.0821

Gnomad FIN AF: 0.0227

Gnomad MID AF: 0.0190

Gnomad NFE AF: 0.0285

Gnomad OTH AF: 0.0415

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

GnomAD4 genome AF: 0.0360 AC: 5479 AN: 152200 Hom.: 441 Cov.: 32 AF XY: 0.0386 AC XY: 2869 AN XY: 74396

Gnomad4 AFR AF: 0.00772

Gnomad4 AMR AF: 0.0333

Gnomad4 ASJ AF: 0.0130

Gnomad4 EAS AF: 0.377

Gnomad4 SAS AF: 0.0814

Gnomad4 FIN AF: 0.0227

Gnomad4 NFE AF: 0.0284

Gnomad4 OTH AF: 0.0425

Alfa AF: 0.0132 Hom.: 5

Bravo AF: 0.0388

Asia WGS AF: 0.182 AC: 632 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.089
DANN	Benign	0.36

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10512300; hg19: chr9-105321871;