rs7024470

Variant names:

• chr9-102559403-A-G
• rs7024470
• ENST00000374801.3:n.74-18868A>G

Variant summary

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

The ENST00000374801.3(LINC00587):​n.74-18868A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0776 in 152,118 control chromosomes in the GnomAD database, including 456 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 (456 hom., cov: 32)
• Consequence: LINC00587 ENST00000374801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0430
• 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.158 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00587	NR_103830.1	n.73-18868A>G		intron_variant	Intron 1 of 4

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00587	ENST00000374801.3	n.74-18868A>G		intron_variant	Intron 1 of 4	1

Frequencies

GnomAD3 genomes AF: 0.0775 AC: 11781 AN: 152000 Hom.: 454 Cov.: 32

Gnomad AFR AF: 0.0849

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0957

Gnomad ASJ AF: 0.0320

Gnomad EAS AF: 0.168

Gnomad SAS AF: 0.0670

Gnomad FIN AF: 0.0807

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0661

Gnomad OTH AF: 0.0647

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

GnomAD4 genome AF: 0.0776 AC: 11801 AN: 152118 Hom.: 456 Cov.: 32 AF XY: 0.0794 AC XY: 5903 AN XY: 74344

African (AFR) AF: 0.0851 AC: 3532 AN: 41528

American (AMR) AF: 0.0962 AC: 1467 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.0320 AC: 111 AN: 3466

East Asian (EAS) AF: 0.168 AC: 864 AN: 5158

South Asian (SAS) AF: 0.0670 AC: 323 AN: 4820

European-Finnish (FIN) AF: 0.0807 AC: 855 AN: 10600

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

European-Non Finnish (NFE) AF: 0.0661 AC: 4496 AN: 67982

Other (OTH) AF: 0.0636 AC: 134 AN: 2108

Alfa AF: 0.0722 Hom.: 80

Bravo AF: 0.0783

Asia WGS AF: 0.102 AC: 353 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.8
DANN	Benign	0.59
PhyloP100		-0.043

Splicing

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

Other links and lift over

dbSNP: rs7024470; hg19: chr9-105321685;