Genetic Variant LINC00683:n.326-30982T>C (chr18-76579863-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 ENST00000583578.6(LINC00683):n.326-30982T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.161 in 152,240 control chromosomes in the GnomAD database, including 1,991 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 0.16 ( 1991 hom., cov: 34)

Consequence

LINC00683
ENST00000583578.6 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.55

Publications

4 publications found

Variant links:

Genes affected

LINC00683 (HGNC:27599): (long intergenic non-protein coding RNA 908)

LINC00683 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=-1.01).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.177 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00683	ENST00000583578.6 link	n.326-30982T>C	intron_variant	Intron 2 of 3	3
LINC00683	ENST00000584910.6 link	n.325-22875T>C	intron_variant	Intron 2 of 2	3
LINC00683	ENST00000651044.1 link	n.176-30982T>C	intron_variant	Intron 2 of 5

Frequencies

GnomAD3 genomes

AF:

0.161

AC:

24444

AN:

152122

Hom.:

1982

Cov.:

show subpopulations

Gnomad AFR

AF:

0.180

Gnomad AMI

AF:

0.172

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.198

Gnomad EAS

AF:

0.182

Gnomad SAS

AF:

0.184

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.168

Gnomad NFE

AF:

0.149

Gnomad OTH

AF:

0.167

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

GnomAD4 genome

AF:

0.161

AC:

24494

AN:

152240

Hom.:

1991

Cov.:

AF XY:

0.160

AC XY:

11907

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.180

AC:

7493

AN:

41542

American (AMR)

AF:

0.156

AC:

2389

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.198

AC:

687

AN:

3472

East Asian (EAS)

AF:

0.182

AC:

943

AN:

5172

South Asian (SAS)

AF:

0.182

AC:

879

AN:

4832

European-Finnish (FIN)

AF:

0.133

AC:

1413

AN:

10606

Middle Eastern (MID)

AF:

0.170

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.149

AC:

10111

AN:

67996

Other (OTH)

AF:

0.176

AC:

372

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1081

2162

3242

4323

5404

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

272

544

816

1088

1360

<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:

0.159

Hom.:

1905

Bravo

AF:

0.164

Asia WGS

AF:

0.227

AC:

791

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

0.40

(source)

DANN

Benign

0.23

PhyloP100

-1.6

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