1-50324208-C-T

Variant names:

• chr1-50324208-C-T
• rs1875645
• ENST00000642061.2:n.114-994G>A

Variant summary

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

The ENST00000642061.2(LINC02808):​n.114-994G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.395 in 151,924 control chromosomes in the GnomAD database, including 12,423 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 0.40 (12423 hom., cov: 32)
• Consequence: LINC02808 ENST00000642061.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.178
• Publications: 4 publications found

Genes affected

LINC02808 (HGNC:54340): (long intergenic non-protein coding RNA 2808)

ENSG00000310470 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000642061.2. 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
	LINC02808	ENST00000642061.2		n.114-994G>A		intron	N/A
	LINC02808	ENST00000850017.1		n.165-994G>A		intron	N/A
	ENSG00000310470	ENST00000850132.1		n.302-723C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.395 AC: 60004 AN: 151804 Hom.: 12411 Cov.: 32

Gnomad AFR AF: 0.346

Gnomad AMI AF: 0.443

Gnomad AMR AF: 0.347

Gnomad ASJ AF: 0.516

Gnomad EAS AF: 0.132

Gnomad SAS AF: 0.399

Gnomad FIN AF: 0.382

Gnomad MID AF: 0.478

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.433

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

GnomAD4 genome AF: 0.395 AC: 60045 AN: 151924 Hom.: 12423 Cov.: 32 AF XY: 0.391 AC XY: 29004 AN XY: 74238

African (AFR) AF: 0.346 AC: 14320 AN: 41400

American (AMR) AF: 0.346 AC: 5281 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.516 AC: 1789 AN: 3470

East Asian (EAS) AF: 0.132 AC: 680 AN: 5162

South Asian (SAS) AF: 0.399 AC: 1916 AN: 4800

European-Finnish (FIN) AF: 0.382 AC: 4029 AN: 10554

Middle Eastern (MID) AF: 0.473 AC: 138 AN: 292

European-Non Finnish (NFE) AF: 0.450 AC: 30569 AN: 67964

Other (OTH) AF: 0.436 AC: 919 AN: 2106

Alfa AF: 0.440 Hom.: 11494

Bravo AF: 0.391

Asia WGS AF: 0.293 AC: 1020 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.0
DANN	Benign	0.78
PhyloP100		-0.18

Splicing

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

Other links and lift over

dbSNP: rs1875645; hg19: chr1-50789880;