rs6718520

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr2-43098432-A-C
• chr2-43098432-A-G
• chr2-43098432-A-T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000434020.2(LINC02580):​n.668-392T>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02580	NR_151714.1	n.412-392T>G		intron_variant	Intron 1 of 1
LOC107985876	XM_047446566.1	c.-3990-392T>G		intron_variant	Intron 1 of 2		XP_047302522.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02580	ENST00000434020.2	n.668-392T>G		intron_variant	Intron 1 of 1	2
LINC02580	ENST00000654095.2	n.197-392T>G		intron_variant	Intron 1 of 1
LINC02580	ENST00000661106.1	n.443-392T>G		intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	4.2
DANN	Benign	0.39
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;