dbSNP rs9380006: LINC01012:n.860+218A>C (chr6-27688720-A-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000783746.1(LINC01012):n.860+218A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 151,652 control chromosomes in the GnomAD database, including 5,898 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 0.26 ( 5898 hom., cov: 30)

Consequence

LINC01012
ENST00000783746.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.583

Publications

8 publications found

Variant links:

Genes affected

LINC01012 (HGNC:48986): (long intergenic non-protein coding RNA 1012)

LINC01012 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=-0.94).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.407 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01012	ENST00000783746.1 link	n.860+218A>C	intron_variant	Intron 1 of 5
LINC01012	ENST00000783747.1 link	n.516+218A>C	intron_variant	Intron 2 of 5
LINC01012	ENST00000783805.1 link	n.*94A>C	downstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.255

AC:

38714

AN:

151532

Hom.:

5887

Cov.:

show subpopulations

Gnomad AFR

AF:

0.413

Gnomad AMI

AF:

0.160

Gnomad AMR

AF:

0.228

Gnomad ASJ

AF:

0.108

Gnomad EAS

AF:

0.364

Gnomad SAS

AF:

0.299

Gnomad FIN

AF:

0.236

Gnomad MID

AF:

0.0791

Gnomad NFE

AF:

0.168

Gnomad OTH

AF:

0.226

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

GnomAD4 genome

AF:

0.256

AC:

38772

AN:

151652

Hom.:

5898

Cov.:

AF XY:

0.260

AC XY:

19277

AN XY:

74104

show subpopulations

African (AFR)

AF:

0.413

AC:

17050

AN:

41326

American (AMR)

AF:

0.228

AC:

3481

AN:

15242

Ashkenazi Jewish (ASJ)

AF:

0.108

AC:

376

AN:

3466

East Asian (EAS)

AF:

0.364

AC:

1880

AN:

5166

South Asian (SAS)

AF:

0.301

AC:

1447

AN:

4812

European-Finnish (FIN)

AF:

0.236

AC:

2454

AN:

10394

Middle Eastern (MID)

AF:

0.0850

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.168

AC:

11443

AN:

67938

Other (OTH)

AF:

0.223

AC:

470

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1312

2623

3935

5246

6558

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

388

776

1164

1552

1940

<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:

0.184

Hom.:

3768

Bravo

AF:

0.263

Asia WGS

AF:

0.318

AC:

1103

AN:

3470

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

2.8

(source)

DANN

Benign

0.28

PhyloP100

-0.58

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