ENST00000304233.3:n.88T>C

Variant names:

• chr8-11576400-T-C
• rs2898290
• ENST00000304233.3:n.88T>C

Variant summary

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

The ENST00000304233.3(LINC00208):​n.88T>C 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 0.481 in 153,118 control chromosomes in the GnomAD database, including 18,835 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 0.48 (18722 hom., cov: 31)
  • Exomes 𝑓: 0.42 (113 hom.)
• Consequence: LINC00208 ENST00000304233.3 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870
• Publications: 46 publications found

Genes affected

LINC00208 (HGNC:15535): (long intergenic non-protein coding RNA 208)

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 = 0.534 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000304233.3. 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
	LINC00208	NR_040035.1		n.-135T>C		upstream_gene	N/A

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00208	ENST00000304233.3	TSL:2	n.88T>C		non_coding_transcript_exon	Exon 1 of 3
	LINC00208	ENST00000652958.1		n.123T>C		non_coding_transcript_exon	Exon 1 of 3
	LINC00208	ENST00000653131.1		n.144T>C		non_coding_transcript_exon	Exon 1 of 2

Frequencies

GnomAD3 genomes AF: 0.482 AC: 73180 AN: 151896 Hom.: 18717 Cov.: 31

Gnomad AFR AF: 0.541

Gnomad AMI AF: 0.347

Gnomad AMR AF: 0.386

Gnomad ASJ AF: 0.618

Gnomad EAS AF: 0.0203

Gnomad SAS AF: 0.294

Gnomad FIN AF: 0.390

Gnomad MID AF: 0.560

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.485

GnomAD4 exome AF: 0.424 AC: 468 AN: 1104 Hom.: 113 Cov.: 0 AF XY: 0.422 AC XY: 258 AN XY: 612

African (AFR) AF: 0.583 AC: 14 AN: 24

American (AMR) AF: 0.400 AC: 4 AN: 10

Ashkenazi Jewish (ASJ) AF: 0.667 AC: 20 AN: 30

East Asian (EAS) AF: 0.0429 AC: 6 AN: 140

South Asian (SAS) AF: 0.400 AC: 4 AN: 10

European-Finnish (FIN) AF: 0.408 AC: 62 AN: 152

Middle Eastern (MID) AF: 0.750 AC: 3 AN: 4

European-Non Finnish (NFE) AF: 0.495 AC: 329 AN: 664

Other (OTH) AF: 0.371 AC: 26 AN: 70

GnomAD4 genome AF: 0.482 AC: 73215 AN: 152014 Hom.: 18722 Cov.: 31 AF XY: 0.467 AC XY: 34701 AN XY: 74316

African (AFR) AF: 0.540 AC: 22401 AN: 41454

American (AMR) AF: 0.386 AC: 5898 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.618 AC: 2147 AN: 3472

East Asian (EAS) AF: 0.0201 AC: 104 AN: 5170

South Asian (SAS) AF: 0.295 AC: 1420 AN: 4808

European-Finnish (FIN) AF: 0.390 AC: 4128 AN: 10584

Middle Eastern (MID) AF: 0.561 AC: 165 AN: 294

European-Non Finnish (NFE) AF: 0.524 AC: 35626 AN: 67934

Other (OTH) AF: 0.480 AC: 1010 AN: 2106

Alfa AF: 0.511 Hom.: 59674

Bravo AF: 0.480

Asia WGS AF: 0.185 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.2
DANN	Benign	0.25
PhyloP100		-0.87

Splicing

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

Other links and lift over

dbSNP: rs2898290; hg19: chr8-11433909;