9-102578059-C-A

Variant names:

• chr9-102578059-C-A
• rs1930551
• ENST00000374801.3:n.74-212C>A

Variant summary

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

The ENST00000374801.3(LINC00587):​n.74-212C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0635 in 152,116 control chromosomes in the GnomAD database, including 347 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 0.063 (347 hom., cov: 32)
• Consequence: LINC00587 ENST00000374801.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.38
• Publications: 5 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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.145 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000374801.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00587	NR_103830.1		n.73-212C>A		intron	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00587	ENST00000374801.3	TSL:1	n.74-212C>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0634 AC: 9638 AN: 151998 Hom.: 343 Cov.: 32

Gnomad AFR AF: 0.0346

Gnomad AMI AF: 0.0143

Gnomad AMR AF: 0.0929

Gnomad ASJ AF: 0.0484

Gnomad EAS AF: 0.155

Gnomad SAS AF: 0.0684

Gnomad FIN AF: 0.0791

Gnomad MID AF: 0.0158

Gnomad NFE AF: 0.0665

Gnomad OTH AF: 0.0556

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

GnomAD4 genome AF: 0.0635 AC: 9655 AN: 152116 Hom.: 347 Cov.: 32 AF XY: 0.0655 AC XY: 4872 AN XY: 74352

African (AFR) AF: 0.0347 AC: 1441 AN: 41528

American (AMR) AF: 0.0933 AC: 1424 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.0484 AC: 168 AN: 3468

East Asian (EAS) AF: 0.154 AC: 796 AN: 5158

South Asian (SAS) AF: 0.0688 AC: 332 AN: 4824

European-Finnish (FIN) AF: 0.0791 AC: 836 AN: 10574

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

European-Non Finnish (NFE) AF: 0.0665 AC: 4524 AN: 67994

Other (OTH) AF: 0.0545 AC: 115 AN: 2110

Alfa AF: 0.0437 Hom.: 48

Bravo AF: 0.0631

Asia WGS AF: 0.0950 AC: 329 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.32
DANN	Benign	0.34
PhyloP100		-1.4

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1930551;

hg19: chr9-105340341;