chr2-242084344-C-T

Variant names:

• chr2-242084344-C-T
• rs749924
• ENST00000824544.1:n.379G>A

Variant summary

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

The ENST00000824544.1(LINC01880):​n.379G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.253 in 148,494 control chromosomes in the GnomAD database, including 5,334 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 0.25 (5334 hom., cov: 30)
• Consequence: LINC01880 ENST00000824544.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 7 publications found

Genes affected

LINC01880 (HGNC:52699): (long intergenic non-protein coding RNA 1880)

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01880	NR_146651.1	n.-206G>A		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01880	ENST00000824544.1	n.379G>A		non_coding_transcript_exon_variant	Exon 1 of 4
LINC01880	ENST00000824545.1	n.256G>A		non_coding_transcript_exon_variant	Exon 1 of 5
LINC01880	ENST00000824550.1	n.405G>A		non_coding_transcript_exon_variant	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.253 AC: 37515 AN: 148380 Hom.: 5314 Cov.: 30

Gnomad AFR AF: 0.447

Gnomad AMI AF: 0.156

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.161

Gnomad EAS AF: 0.435

Gnomad SAS AF: 0.348

Gnomad FIN AF: 0.174

Gnomad MID AF: 0.215

Gnomad NFE AF: 0.117

Gnomad OTH AF: 0.241

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

GnomAD4 genome AF: 0.253 AC: 37582 AN: 148494 Hom.: 5334 Cov.: 30 AF XY: 0.259 AC XY: 18770 AN XY: 72484

African (AFR) AF: 0.447 AC: 17593 AN: 39332

American (AMR) AF: 0.348 AC: 5204 AN: 14944

Ashkenazi Jewish (ASJ) AF: 0.161 AC: 552 AN: 3418

East Asian (EAS) AF: 0.434 AC: 2188 AN: 5036

South Asian (SAS) AF: 0.346 AC: 1613 AN: 4658

European-Finnish (FIN) AF: 0.174 AC: 1823 AN: 10474

Middle Eastern (MID) AF: 0.214 AC: 63 AN: 294

European-Non Finnish (NFE) AF: 0.117 AC: 7901 AN: 67380

Other (OTH) AF: 0.246 AC: 503 AN: 2048

Alfa AF: 0.208 Hom.: 482

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	0.69
DANN	Benign	0.63
PhyloP100		-2.5

Splicing

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

Other links and lift over

dbSNP: rs749924; hg19: chr2-243026495; COSMIC: COSV68998294;