rs2409798

Variant names:

• chr8-11578055-C-T
• rs2409798
• ENST00000652958.1:n.1168C>T

Variant summary

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

The ENST00000652958.1(LINC00208):​n.1168C>T 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 0.429 in 152,004 control chromosomes in the GnomAD database, including 15,080 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 0.43 (15080 hom., cov: 32)
• Consequence: LINC00208 ENST00000652958.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.670
• Publications: 14 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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000652958.1. 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
	LINC00208	NR_040035.1		n.784-315C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC00208	ENST00000652958.1		n.1168C>T		non_coding_transcript_exon	Exon 3 of 3
	LINC00208	ENST00000653131.1		n.1238C>T		non_coding_transcript_exon	Exon 2 of 2
	LINC00208	ENST00000304233.3	TSL:2	n.1006-315C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.429 AC: 65148 AN: 151886 Hom.: 15079 Cov.: 32

Gnomad AFR AF: 0.358

Gnomad AMI AF: 0.348

Gnomad AMR AF: 0.365

Gnomad ASJ AF: 0.617

Gnomad EAS AF: 0.0191

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.388

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.524

Gnomad OTH AF: 0.451

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

GnomAD4 genome AF: 0.429 AC: 65164 AN: 152004 Hom.: 15080 Cov.: 32 AF XY: 0.416 AC XY: 30871 AN XY: 74288

African (AFR) AF: 0.358 AC: 14848 AN: 41464

American (AMR) AF: 0.364 AC: 5567 AN: 15276

Ashkenazi Jewish (ASJ) AF: 0.617 AC: 2137 AN: 3464

East Asian (EAS) AF: 0.0189 AC: 98 AN: 5172

South Asian (SAS) AF: 0.294 AC: 1416 AN: 4814

European-Finnish (FIN) AF: 0.388 AC: 4103 AN: 10576

Middle Eastern (MID) AF: 0.555 AC: 162 AN: 292

European-Non Finnish (NFE) AF: 0.524 AC: 35576 AN: 67926

Other (OTH) AF: 0.445 AC: 940 AN: 2110

Alfa AF: 0.500 Hom.: 11184

Bravo AF: 0.419

Asia WGS AF: 0.172 AC: 604 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	0.71
DANN	Benign	0.74
PhyloP100		-0.67

Splicing

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

Other links and lift over

dbSNP: rs2409798; hg19: chr8-11435564;