ENST00000850026.1:n.509G>A

Variant names:

• chr1-50328624-C-T
• rs1948808
• ENST00000850026.1:n.509G>A

Variant summary

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

The ENST00000850026.1(LINC02808):​n.509G>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 0.468 in 151,908 control chromosomes in the GnomAD database, including 17,317 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 0.47 (17317 hom., cov: 32)
• Consequence: LINC02808 ENST00000850026.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.308
• Publications: 4 publications found

Genes affected

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

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000850026.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC02808	ENST00000850026.1		n.509G>A		non_coding_transcript_exon	Exon 2 of 2
	LINC02808	ENST00000642061.2		n.113+4881G>A		intron	N/A
	LINC02808	ENST00000850017.1		n.164+4881G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.468 AC: 71041 AN: 151790 Hom.: 17291 Cov.: 32

Gnomad AFR AF: 0.551

Gnomad AMI AF: 0.445

Gnomad AMR AF: 0.380

Gnomad ASJ AF: 0.541

Gnomad EAS AF: 0.133

Gnomad SAS AF: 0.414

Gnomad FIN AF: 0.394

Gnomad MID AF: 0.532

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.494

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

GnomAD4 genome AF: 0.468 AC: 71115 AN: 151908 Hom.: 17317 Cov.: 32 AF XY: 0.460 AC XY: 34157 AN XY: 74228

African (AFR) AF: 0.551 AC: 22829 AN: 41412

American (AMR) AF: 0.379 AC: 5788 AN: 15264

Ashkenazi Jewish (ASJ) AF: 0.541 AC: 1877 AN: 3468

East Asian (EAS) AF: 0.133 AC: 686 AN: 5170

South Asian (SAS) AF: 0.413 AC: 1987 AN: 4806

European-Finnish (FIN) AF: 0.394 AC: 4156 AN: 10536

Middle Eastern (MID) AF: 0.537 AC: 158 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32179 AN: 67936

Other (OTH) AF: 0.497 AC: 1051 AN: 2114

Alfa AF: 0.472 Hom.: 2451

Bravo AF: 0.471

Asia WGS AF: 0.323 AC: 1122 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	8.1
DANN	Benign	0.65
PhyloP100		0.31

Splicing

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

Other links and lift over

dbSNP: rs1948808; hg19: chr1-50794296;