rs2374482

Variant names:

• chr2-43078788-G-A
• rs2374482
• XM_047446566.1:c.-3907-6228C>T

Variant summary

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

The ENST00000716701.1(LINC02580):​n.398+19170C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.374 in 152,098 control chromosomes in the GnomAD database, including 10,910 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 0.37 (10910 hom., cov: 33)
• Consequence: LINC02580 ENST00000716701.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.161
• Publications: 1 publications found

Genes affected

LOC107985876 (HGNC:):

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

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 (AFR) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000716701.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02580	ENST00000716701.1		n.398+19170C>T		intron	N/A
	LINC02580	ENST00000716702.1		n.461-6228C>T		intron	N/A
	ENSG00000307929	ENST00000829890.1		n.327-404G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.374 AC: 56868 AN: 151980 Hom.: 10913 Cov.: 33

Gnomad AFR AF: 0.441

Gnomad AMI AF: 0.308

Gnomad AMR AF: 0.290

Gnomad ASJ AF: 0.341

Gnomad EAS AF: 0.106

Gnomad SAS AF: 0.277

Gnomad FIN AF: 0.336

Gnomad MID AF: 0.446

Gnomad NFE AF: 0.388

Gnomad OTH AF: 0.368

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

GnomAD4 genome AF: 0.374 AC: 56888 AN: 152098 Hom.: 10910 Cov.: 33 AF XY: 0.367 AC XY: 27257 AN XY: 74364

African (AFR) AF: 0.441 AC: 18298 AN: 41498

American (AMR) AF: 0.290 AC: 4423 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.341 AC: 1183 AN: 3472

East Asian (EAS) AF: 0.105 AC: 545 AN: 5170

South Asian (SAS) AF: 0.275 AC: 1324 AN: 4816

European-Finnish (FIN) AF: 0.336 AC: 3562 AN: 10594

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.388 AC: 26365 AN: 67956

Other (OTH) AF: 0.367 AC: 775 AN: 2112

Alfa AF: 0.377 Hom.: 47657

Bravo AF: 0.372

Asia WGS AF: 0.206 AC: 717 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	0.68
DANN	Benign	0.36
PhyloP100		-0.16

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: rs2374482;

hg19: chr2-43305926;