rs10990158

Variant names:

• chr9-102533824-T-A
• rs10990158
• ENST00000374801.3:n.73+14116T>A

Variant summary

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

The ENST00000374801.3(LINC00587):​n.73+14116T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0578 in 151,964 control chromosomes in the GnomAD database, including 328 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 0.058 (328 hom., cov: 32)
• Consequence: LINC00587 ENST00000374801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.04
• Publications: 1 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00587	NR_103830.1	n.72+14116T>A		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00587	ENST00000374801.3	n.73+14116T>A		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes AF: 0.0579 AC: 8785 AN: 151846 Hom.: 327 Cov.: 32

Gnomad AFR AF: 0.0139

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0854

Gnomad ASJ AF: 0.0305

Gnomad EAS AF: 0.176

Gnomad SAS AF: 0.0737

Gnomad FIN AF: 0.0800

Gnomad MID AF: 0.00949

Gnomad NFE AF: 0.0675

Gnomad OTH AF: 0.0489

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

GnomAD4 genome AF: 0.0578 AC: 8789 AN: 151964 Hom.: 328 Cov.: 32 AF XY: 0.0604 AC XY: 4486 AN XY: 74266

African (AFR) AF: 0.0139 AC: 575 AN: 41510

American (AMR) AF: 0.0860 AC: 1309 AN: 15224

Ashkenazi Jewish (ASJ) AF: 0.0305 AC: 106 AN: 3470

East Asian (EAS) AF: 0.175 AC: 892 AN: 5098

South Asian (SAS) AF: 0.0740 AC: 357 AN: 4824

European-Finnish (FIN) AF: 0.0800 AC: 848 AN: 10600

Middle Eastern (MID) AF: 0.0102 AC: 3 AN: 294

European-Non Finnish (NFE) AF: 0.0675 AC: 4585 AN: 67924

Other (OTH) AF: 0.0479 AC: 101 AN: 2108

Alfa AF: 0.0601 Hom.: 46

Bravo AF: 0.0560

Asia WGS AF: 0.0980 AC: 338 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.12
DANN	Benign	0.65
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs10990158; hg19: chr9-105296106;