Genetic Variant LINC00609:n.289-263G>C (chr14-35998147-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000550089.2(LINC00609):n.289-263G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0819 in 152,194 control chromosomes in the GnomAD database, including 895 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 0.082 ( 895 hom., cov: 32)

Consequence

LINC00609
ENST00000550089.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0570

Publications

3 publications found

Variant links:

Genes affected

LINC00609 (HGNC:43960): (long intergenic non-protein coding RNA 609)

LINC00609 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=-0.85).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.188 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
LINC00609	ENST00000550089.2 link	n.289-263G>C	intron_variant	Intron 2 of 4	3
LINC00609	ENST00000660969.2 link	n.341-263G>C	intron_variant	Intron 2 of 3
LINC00609	ENST00000662718.2 link	n.177-263G>C	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.0819

AC:

12457

AN:

152076

Hom.:

892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.192

Gnomad AMI

AF:

0.0407

Gnomad AMR

AF:

0.0604

Gnomad ASJ

AF:

0.0334

Gnomad EAS

AF:

0.0942

Gnomad SAS

AF:

0.0681

Gnomad FIN

AF:

0.0300

Gnomad MID

AF:

0.0411

Gnomad NFE

AF:

0.0319

Gnomad OTH

AF:

0.0559

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

GnomAD4 genome

AF:

0.0819

AC:

12467

AN:

152194

Hom.:

895

Cov.:

AF XY:

0.0806

AC XY:

5998

AN XY:

74408

show subpopulations

African (AFR)

AF:

0.192

AC:

7957

AN:

41484

American (AMR)

AF:

0.0603

AC:

922

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.0334

AC:

116

AN:

3472

East Asian (EAS)

AF:

0.0946

AC:

490

AN:

5178

South Asian (SAS)

AF:

0.0677

AC:

326

AN:

4814

European-Finnish (FIN)

AF:

0.0300

AC:

318

AN:

10612

Middle Eastern (MID)

AF:

0.0442

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0319

AC:

2171

AN:

68022

Other (OTH)

AF:

0.0553

AC:

117

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

554

1108

1663

2217

2771

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

140

280

420

560

700

<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:

0.0120

Hom.:

Bravo

AF:

0.0912

Asia WGS

AF:

0.105

AC:

365

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.65

(source)

DANN

Benign

0.61

PhyloP100

-0.057

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