ENST00000786158.1:n.630-430A>G

Variant names:

• chr18-73391387-A-G
• rs1943816
• ENST00000786158.1:n.630-430A>G

Variant summary

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

The ENST00000786158.1(LINC02582):​n.630-430A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 151,780 control chromosomes in the GnomAD database, including 2,851 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 0.17 (2851 hom., cov: 32)
• Consequence: LINC02582 ENST00000786158.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.07
• Publications: 12 publications found

Genes affected

LINC02582 (HGNC:53792): (long intergenic non-protein coding RNA 2582)

LOC105372190 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.293 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000786158.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02582	ENST00000786158.1		n.630-430A>G		intron	N/A
	LINC02582	ENST00000786159.1		n.718-430A>G		intron	N/A
	LINC02582	ENST00000786160.1		n.716-430A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.173 AC: 26232 AN: 151662 Hom.: 2845 Cov.: 32

Gnomad AFR AF: 0.298

Gnomad AMI AF: 0.169

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.0995

Gnomad EAS AF: 0.215

Gnomad SAS AF: 0.132

Gnomad FIN AF: 0.106

Gnomad MID AF: 0.133

Gnomad NFE AF: 0.123

Gnomad OTH AF: 0.155

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

GnomAD4 genome AF: 0.173 AC: 26263 AN: 151780 Hom.: 2851 Cov.: 32 AF XY: 0.171 AC XY: 12696 AN XY: 74196

African (AFR) AF: 0.297 AC: 12242 AN: 41154

American (AMR) AF: 0.124 AC: 1897 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.0995 AC: 345 AN: 3468

East Asian (EAS) AF: 0.216 AC: 1115 AN: 5158

South Asian (SAS) AF: 0.132 AC: 635 AN: 4822

European-Finnish (FIN) AF: 0.106 AC: 1122 AN: 10598

Middle Eastern (MID) AF: 0.133 AC: 39 AN: 294

European-Non Finnish (NFE) AF: 0.123 AC: 8385 AN: 68000

Other (OTH) AF: 0.156 AC: 329 AN: 2106

Alfa AF: 0.143 Hom.: 4406

Bravo AF: 0.178

Asia WGS AF: 0.194 AC: 674 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.75
DANN	Benign	0.74
PhyloP100		-1.1

Splicing

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

Other links and lift over

dbSNP: rs1943816; hg19: chr18-71058622;