chr3-34434774-T-A

Variant names:

• chr3-34434774-T-A
• rs1114855
• ENST00000424786.5:n.570+25425T>A

Variant summary

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

The ENST00000424786.5(LINC01811):​n.570+25425T>A variant causes a intron 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 ENST00000424786.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.374
• Publications: 2 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000424786.5. 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
	LINC01811	NR_183676.1		n.393-519T>A		intron	N/A
	LINC01811	NR_183677.1		n.354-519T>A		intron	N/A
	LINC01811	NR_183678.1		n.197-519T>A		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01811	ENST00000424786.5	TSL:5	n.570+25425T>A		intron	N/A
	LINC01811	ENST00000655439.1		n.242-519T>A		intron	N/A
	LINC01811	ENST00000655650.1		n.309+25425T>A		intron	N/A

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

African (AFR) AF: 0.360 AC: 14933 AN: 41488

American (AMR) AF: 0.482 AC: 7369 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.366 AC: 1272 AN: 3472

East Asian (EAS) AF: 0.516 AC: 2652 AN: 5140

South Asian (SAS) AF: 0.505 AC: 2438 AN: 4824

European-Finnish (FIN) AF: 0.396 AC: 4180 AN: 10550

Middle Eastern (MID) AF: 0.323 AC: 95 AN: 294

European-Non Finnish (NFE) AF: 0.385 AC: 26193 AN: 67960

Other (OTH) AF: 0.407 AC: 858 AN: 2108

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	4.1
DANN	Benign	0.68
PhyloP100		0.37

Splicing

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

Other links and lift over

dbSNP: rs1114855; hg19: chr3-34476266;