3-34421377-C-T

Variant names:

• chr3-34421377-C-T
• rs11714343
• ENST00000424786.5:n.570+12028C>T

Variant summary

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

The ENST00000424786.5(LINC01811):​n.570+12028C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0611 in 152,178 control chromosomes in the GnomAD database, including 430 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 0.061 (430 hom., cov: 32)
• Consequence: LINC01811 ENST00000424786.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740
• Publications: 3 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=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0838 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.392+12016C>T		intron	N/A
	LINC01811	NR_183677.1		n.353+12028C>T		intron	N/A
	LINC01811	NR_183678.1		n.197-13916C>T		intron	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01811	ENST00000424786.5	TSL:5	n.570+12028C>T		intron	N/A
	LINC01811	ENST00000655439.1		n.241+12016C>T		intron	N/A
	LINC01811	ENST00000655650.1		n.309+12028C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.0611 AC: 9294 AN: 152060 Hom.: 430 Cov.: 32

Gnomad AFR AF: 0.0142

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0541

Gnomad ASJ AF: 0.165

Gnomad EAS AF: 0.000962

Gnomad SAS AF: 0.0584

Gnomad FIN AF: 0.0942

Gnomad MID AF: 0.104

Gnomad NFE AF: 0.0857

Gnomad OTH AF: 0.0589

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

GnomAD4 genome AF: 0.0611 AC: 9293 AN: 152178 Hom.: 430 Cov.: 32 AF XY: 0.0613 AC XY: 4556 AN XY: 74372

African (AFR) AF: 0.0142 AC: 591 AN: 41542

American (AMR) AF: 0.0540 AC: 825 AN: 15282

Ashkenazi Jewish (ASJ) AF: 0.165 AC: 572 AN: 3466

East Asian (EAS) AF: 0.000965 AC: 5 AN: 5184

South Asian (SAS) AF: 0.0585 AC: 281 AN: 4804

European-Finnish (FIN) AF: 0.0942 AC: 996 AN: 10576

Middle Eastern (MID) AF: 0.0986 AC: 29 AN: 294

European-Non Finnish (NFE) AF: 0.0857 AC: 5826 AN: 68008

Other (OTH) AF: 0.0588 AC: 124 AN: 2110

Alfa AF: 0.0785 Hom.: 364

Bravo AF: 0.0559

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
CADD	Benign	5.8
DANN	Benign	0.74
PhyloP100		-0.074
Mutation Taster		=100/0	polymorphism

Splicing

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

Other links and lift over

dbSNP: rs11714343; hg19: chr3-34462869;