rs2898290

chr8-11576400-T-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000661938.1(LINC00208):n.111T>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 ENST00000661938.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.870

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC00208	ENST00000661938.1	n.111T>C		non_coding_transcript_exon_variant	1/4

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

Gnomad4 AFR exome AF: 0.583

Gnomad4 AMR exome AF: 0.400

Gnomad4 ASJ exome AF: 0.667

Gnomad4 EAS exome AF: 0.0429

Gnomad4 SAS exome AF: 0.400

Gnomad4 FIN exome AF: 0.408

Gnomad4 NFE exome AF: 0.495

Gnomad4 OTH exome AF: 0.371

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

Gnomad4 AFR AF: 0.540

Gnomad4 AMR AF: 0.386

Gnomad4 ASJ AF: 0.618

Gnomad4 EAS AF: 0.0201

Gnomad4 SAS AF: 0.295

Gnomad4 FIN AF: 0.390

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.480

Alfa AF: 0.517 Hom.: 26145

Bravo AF: 0.480

Asia WGS AF: 0.185 AC: 648 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	1.2
Dann	Benign	0.25

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2898290; hg19: chr8-11433909;