XM_017005460.2:c.*1348C>T

Variant names:

• chr2-43065694-G-A
• rs2374459
• XM_017005460.2:c.*1348C>T

Variant summary

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

The XM_017005460.2(LOC107985876):​c.*1348C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 152,054 control chromosomes in the GnomAD database, including 23,364 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 0.54 (23364 hom., cov: 32)
• Consequence: LOC107985876 XM_017005460.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.03
• Publications: 0 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=-0.95).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.625 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC107985876	XM_017005460.2	c.*1348C>T		3_prime_UTR_variant	Exon 2 of 2		XP_016860949.1
LOC107985876	XM_047446566.1	c.*2039C>T		3_prime_UTR_variant	Exon 3 of 3		XP_047302522.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02580	ENST00000716701.1	n.399-28929C>T		intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81499 AN: 151936 Hom.: 23364 Cov.: 32

Gnomad AFR AF: 0.336

Gnomad AMI AF: 0.621

Gnomad AMR AF: 0.596

Gnomad ASJ AF: 0.595

Gnomad EAS AF: 0.384

Gnomad SAS AF: 0.482

Gnomad FIN AF: 0.699

Gnomad MID AF: 0.608

Gnomad NFE AF: 0.630

Gnomad OTH AF: 0.546

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

GnomAD4 genome AF: 0.536 AC: 81524 AN: 152054 Hom.: 23364 Cov.: 32 AF XY: 0.539 AC XY: 40074 AN XY: 74346

African (AFR) AF: 0.336 AC: 13909 AN: 41430

American (AMR) AF: 0.597 AC: 9116 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.595 AC: 2061 AN: 3464

East Asian (EAS) AF: 0.384 AC: 1986 AN: 5170

South Asian (SAS) AF: 0.481 AC: 2319 AN: 4824

European-Finnish (FIN) AF: 0.699 AC: 7401 AN: 10584

Middle Eastern (MID) AF: 0.616 AC: 181 AN: 294

European-Non Finnish (NFE) AF: 0.630 AC: 42833 AN: 67984

Other (OTH) AF: 0.546 AC: 1155 AN: 2116

Alfa AF: 0.588 Hom.: 80112

Bravo AF: 0.521

Asia WGS AF: 0.435 AC: 1514 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.028
DANN	Benign	0.59
PhyloP100		-2.0

Splicing

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

Other links and lift over

dbSNP: rs2374459; hg19: chr2-43292832;