rs2409798

Variant names:

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

Variant summary

Our verdict is Benign. Variant got -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

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.519 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC00208	NR_040035.1	n.784-315C>T		intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC00208	ENST00000652958.1	n.1168C>T		non_coding_transcript_exon_variant	Exon 3 of 3
LINC00208	ENST00000653131.1	n.1238C>T		non_coding_transcript_exon_variant	Exon 2 of 2
LINC00208	ENST00000304233.3	n.1006-315C>T		intron_variant	Intron 1 of 2	2

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

Gnomad4 AFR AF: 0.358

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.617

Gnomad4 EAS AF: 0.0189

Gnomad4 SAS AF: 0.294

Gnomad4 FIN AF: 0.388

Gnomad4 NFE AF: 0.524

Gnomad4 OTH AF: 0.445

Alfa AF: 0.499 Hom.: 10068

Bravo AF: 0.419

Asia WGS AF: 0.172 AC: 604 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	0.71
DANN	Benign	0.74

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2409798; hg19: chr8-11435564;