Genetic Variant ENST00000415991.2:n.36-171T>C (chr3-34170674-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000415991.2(LINC01811):n.36-171T>C variant causes a intron 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
ENST00000415991.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.74

Publications

10 publications found

Variant links:

Genes affected

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

LINC01811 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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	Effect	Exon rank
LINC01811	NR_183676.1 link	n.81-171T>C	intron_variant	Intron 1 of 5
LINC01811	NR_183677.1 link	n.54-171T>C	intron_variant	Intron 1 of 5
LINC01811	NR_183678.1 link	n.54-171T>C	intron_variant	Intron 1 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01811	ENST00000415991.2 link	n.36-171T>C	intron_variant	Intron 1 of 5	5
LINC01811	ENST00000424786.5 link	n.84-171T>C	intron_variant	Intron 1 of 7	5
LINC01811	ENST00000654751.1 link	n.842-128179T>C	intron_variant	Intron 3 of 5

Frequencies

GnomAD3 genomes

AF:

0.668

AC:

101501

AN:

151936

Hom.:

34987

Cov.:

show subpopulations

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.:

AF XY:

0.664

AC XY:

49330

AN XY:

74318

show subpopulations

African (AFR)

AF:

0.625

AC:

25905

AN:

41470

American (AMR)

AF:

0.712

AC:

10889

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.804

AC:

2790

AN:

3470

East Asian (EAS)

AF:

0.124

AC:

643

AN:

5166

South Asian (SAS)

AF:

0.535

AC:

2573

AN:

4812

European-Finnish (FIN)

AF:

0.685

AC:

7231

AN:

10556

Middle Eastern (MID)

AF:

0.687

AC:

202

AN:

294

European-Non Finnish (NFE)

AF:

0.725

AC:

49269

AN:

67974

Other (OTH)

AF:

0.679

AC:

1435

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1624

3248

4871

6495

8119

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

788

1576

2364

3152

3940

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.701

Hom.:

84145

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

(source)

DANN

Benign

0.53

PhyloP100

-1.7

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over