rs11714343

chr3-34421377-C-T

Variant summary

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

The NR_183677.1(LINC01811):n.353+12028C>T 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 0.0611 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 NR_183677.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0740

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=-0.68).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0838 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
LINC01811	NR_183677.1	n.353+12028C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
LINC01811	ENST00000659779.1	n.378+12028C>T		intron_variant, non_coding_transcript_variant

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

Gnomad4 AFR AF: 0.0142

Gnomad4 AMR AF: 0.0540

Gnomad4 ASJ AF: 0.165

Gnomad4 EAS AF: 0.000965

Gnomad4 SAS AF: 0.0585

Gnomad4 FIN AF: 0.0942

Gnomad4 NFE AF: 0.0857

Gnomad4 OTH AF: 0.0588

Alfa AF: 0.0814 Hom.: 273

Bravo AF: 0.0559

Asia WGS AF: 0.0270 AC: 94 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.68
Cadd	Benign	5.8
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: rs11714343; hg19: chr3-34462869;