rs2374482

Variant names:

• chr2-43078788-G-A
• rs2374482
• ENST00000716701.1:n.398+19170C>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

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

ENSG00000307929 (HGNC:):

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985876	XM_047446566.1	c.-3907-6228C>T		intron_variant	Intron 2 of 2		XP_047302522.1
LOC124907756	XR_007086299.1	n.226-404G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02580	ENST00000716701.1	n.398+19170C>T		intron_variant	Intron 2 of 4
LINC02580	ENST00000716702.1	n.461-6228C>T		intron_variant	Intron 2 of 2
ENSG00000307929	ENST00000829890.1	n.327-404G>A		intron_variant	Intron 1 of 1

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 v4.3

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

Other links and lift over

dbSNP: rs2374482; hg19: chr2-43305926;