rs7039568

Variant names:

• chr9-102559501-C-T
• rs7039568
• ENST00000374801.3:n.74-18770C>T

Variant summary

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

The ENST00000374801.3(LINC00587):​n.74-18770C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0778 in 152,010 control chromosomes in the GnomAD database, including 460 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 0.078 (460 hom., cov: 32)
• Consequence: LINC00587 ENST00000374801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.13
• Publications: 2 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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.159 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00587	NR_103830.1	n.73-18770C>T		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00587	ENST00000374801.3	n.74-18770C>T		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes AF: 0.0777 AC: 11805 AN: 151892 Hom.: 458 Cov.: 32

Gnomad AFR AF: 0.0852

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0323

Gnomad EAS AF: 0.169

Gnomad SAS AF: 0.0674

Gnomad FIN AF: 0.0814

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0662

Gnomad OTH AF: 0.0652

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

GnomAD4 genome AF: 0.0778 AC: 11825 AN: 152010 Hom.: 460 Cov.: 32 AF XY: 0.0797 AC XY: 5926 AN XY: 74316

African (AFR) AF: 0.0853 AC: 3538 AN: 41476

American (AMR) AF: 0.0962 AC: 1467 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.0323 AC: 112 AN: 3470

East Asian (EAS) AF: 0.169 AC: 869 AN: 5154

South Asian (SAS) AF: 0.0675 AC: 325 AN: 4818

European-Finnish (FIN) AF: 0.0814 AC: 860 AN: 10562

Middle Eastern (MID) AF: 0.0204 AC: 6 AN: 294

European-Non Finnish (NFE) AF: 0.0662 AC: 4500 AN: 67968

Other (OTH) AF: 0.0640 AC: 135 AN: 2108

Alfa AF: 0.0715 Hom.: 74

Bravo AF: 0.0783

Asia WGS AF: 0.102 AC: 354 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.54
DANN	Benign	0.27
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs7039568; hg19: chr9-105321783;