2-43098432-A-G

Variant names:

• chr2-43098432-A-G
• rs6718520
• ENST00000434020.2:n.668-392T>C

Variant summary

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

The ENST00000434020.2(LINC02580):​n.668-392T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.642 in 151,984 control chromosomes in the GnomAD database, including 33,034 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 0.64 (33034 hom., cov: 30)
• Consequence: LINC02580 ENST00000434020.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.734
• Publications: 27 publications found

Genes affected

LINC02580 (HGNC:53751): (long intergenic non-protein coding RNA 2580)

LOC107985876 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.861 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000434020.2. 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
	LINC02580	NR_151714.1		n.412-392T>C		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02580	ENST00000434020.2	TSL:2	n.668-392T>C		intron	N/A
	LINC02580	ENST00000654095.2		n.197-392T>C		intron	N/A
	LINC02580	ENST00000661106.1		n.443-392T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.641 AC: 97376 AN: 151866 Hom.: 32967 Cov.: 30

Gnomad AFR AF: 0.868

Gnomad AMI AF: 0.603

Gnomad AMR AF: 0.633

Gnomad ASJ AF: 0.568

Gnomad EAS AF: 0.753

Gnomad SAS AF: 0.535

Gnomad FIN AF: 0.519

Gnomad MID AF: 0.671

Gnomad NFE AF: 0.527

Gnomad OTH AF: 0.655

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

GnomAD4 genome AF: 0.642 AC: 97501 AN: 151984 Hom.: 33034 Cov.: 30 AF XY: 0.641 AC XY: 47619 AN XY: 74272

African (AFR) AF: 0.869 AC: 36024 AN: 41474

American (AMR) AF: 0.634 AC: 9682 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.568 AC: 1970 AN: 3470

East Asian (EAS) AF: 0.753 AC: 3868 AN: 5134

South Asian (SAS) AF: 0.535 AC: 2574 AN: 4810

European-Finnish (FIN) AF: 0.519 AC: 5486 AN: 10570

Middle Eastern (MID) AF: 0.684 AC: 201 AN: 294

European-Non Finnish (NFE) AF: 0.527 AC: 35771 AN: 67934

Other (OTH) AF: 0.653 AC: 1376 AN: 2106

Alfa AF: 0.565 Hom.: 79732

Bravo AF: 0.667

Asia WGS AF: 0.663 AC: 2309 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	3.9
DANN	Benign	0.45
PhyloP100		0.73

Splicing

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

Other links and lift over

dbSNP: rs6718520; hg19: chr2-43325570;