rs1114855

Positions:

• chr3-34434774-T-A
• chr3-34434774-T-C
• chr3-34434774-T-G

Variant summary

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

The NR_183677.1(LINC01811):​n.354-519T>A variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.397 in 152,026 control chromosomes in the GnomAD database, including 12,107 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 0.40 (12107 hom., cov: 32)
• Consequence: LINC01811 NR_183677.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374

Genes affected

LINC01811 (HGNC:52615): (long intergenic non-protein coding RNA 1811)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.5 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01811	NR_183677.1	n.354-519T>A		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01811	ENST00000659779.1	n.378+25425T>A		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.397 AC: 60306 AN: 151908 Hom.: 12104 Cov.: 32

Gnomad AFR AF: 0.360

Gnomad AMI AF: 0.393

Gnomad AMR AF: 0.482

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.515

Gnomad SAS AF: 0.506

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.329

Gnomad NFE AF: 0.385

Gnomad OTH AF: 0.405

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

GnomAD4 genome AF: 0.397 AC: 60348 AN: 152026 Hom.: 12107 Cov.: 32 AF XY: 0.401 AC XY: 29815 AN XY: 74312

Gnomad4 AFR AF: 0.360

Gnomad4 AMR AF: 0.482

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.516

Gnomad4 SAS AF: 0.505

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.385

Gnomad4 OTH AF: 0.407

Alfa AF: 0.404 Hom.: 1541

Bravo AF: 0.401

Asia WGS AF: 0.475 AC: 1650 AN: 3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.1
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1114855; hg19: chr3-34476266;