3-34170674-T-C

Position:

• chr3-34170674-T-C

Variant summary

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

The NR_183677.1(LINC01811):​n.54-171T>C 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 0.668 in 152,054 control chromosomes in the GnomAD database, including 35,017 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 0.67 (35017 hom., cov: 32)
• Consequence: LINC01811 NR_183677.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.74

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=-0.97).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.719 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
LINC01811	NR_183677.1	n.54-171T>C		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
LINC01811	ENST00000415991.2	n.36-171T>C		intron_variant, non_coding_transcript_variant		5
LINC01811	ENST00000424786.5	n.84-171T>C		intron_variant, non_coding_transcript_variant		5
LINC01811	ENST00000654751.1	n.842-128179T>C		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.668 AC: 101501 AN: 151936 Hom.: 34987 Cov.: 32

Gnomad AFR AF: 0.625

Gnomad AMI AF: 0.698

Gnomad AMR AF: 0.712

Gnomad ASJ AF: 0.804

Gnomad EAS AF: 0.125

Gnomad SAS AF: 0.536

Gnomad FIN AF: 0.685

Gnomad MID AF: 0.680

Gnomad NFE AF: 0.725

Gnomad OTH AF: 0.684

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

GnomAD4 genome AF: 0.668 AC: 101572 AN: 152054 Hom.: 35017 Cov.: 32 AF XY: 0.664 AC XY: 49330 AN XY: 74318

Gnomad4 AFR AF: 0.625

Gnomad4 AMR AF: 0.712

Gnomad4 ASJ AF: 0.804

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.535

Gnomad4 FIN AF: 0.685

Gnomad4 NFE AF: 0.725

Gnomad4 OTH AF: 0.679

Alfa AF: 0.705 Hom.: 51552

Bravo AF: 0.667

Asia WGS AF: 0.381 AC: 1328 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.84
DANN	Benign	0.53

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs6781182; hg19: chr3-34212166;