dbSNP rs1472716: LINC02336:n.112-582A>G (chr13-89413849-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000659314.1(LINC02336):n.112-582A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.177 in 152,102 control chromosomes in the GnomAD database, including 2,652 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 0.18 ( 2652 hom., cov: 32)

Consequence

LINC02336
ENST00000659314.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.276

Publications

4 publications found

Variant links:

Genes affected

LINC02336 (HGNC:53256): (long intergenic non-protein coding RNA 2336)

LINC02336 links:

LOC107984621 (HGNC:):

LOC107984621 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=-1.03).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LOC107984621	XR_001749952.2 link	n.64-582A>G	intron_variant	Intron 1 of 2
LOC107984621	XR_001749953.2 link	n.198-582A>G	intron_variant	Intron 2 of 3
LOC107984621	XR_001749954.2 link	n.260-582A>G	intron_variant	Intron 2 of 3

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02336	ENST00000659314.1 link	n.112-582A>G	intron_variant	Intron 1 of 3
LINC02336	ENST00000670662.1 link	n.260-582A>G	intron_variant	Intron 2 of 5
LINC02336	ENST00000795232.1 link	n.200-582A>G	intron_variant	Intron 2 of 4

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26816

AN:

151984

Hom.:

2644

Cov.:

show subpopulations

Gnomad AFR

AF:

0.254

Gnomad AMI

AF:

0.117

Gnomad AMR

AF:

0.155

Gnomad ASJ

AF:

0.269

Gnomad EAS

AF:

0.0476

Gnomad SAS

AF:

0.147

Gnomad FIN

AF:

0.0866

Gnomad MID

AF:

0.285

Gnomad NFE

AF:

0.155

Gnomad OTH

AF:

0.192

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

GnomAD4 genome

AF:

0.177

AC:

26855

AN:

152102

Hom.:

2652

Cov.:

AF XY:

0.173

AC XY:

12847

AN XY:

74374

show subpopulations

African (AFR)

AF:

0.254

AC:

10549

AN:

41464

American (AMR)

AF:

0.155

AC:

2363

AN:

15288

Ashkenazi Jewish (ASJ)

AF:

0.269

AC:

935

AN:

3470

East Asian (EAS)

AF:

0.0473

AC:

244

AN:

5156

South Asian (SAS)

AF:

0.147

AC:

707

AN:

4810

European-Finnish (FIN)

AF:

0.0866

AC:

919

AN:

10606

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.155

AC:

10543

AN:

67990

Other (OTH)

AF:

0.190

AC:

401

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1072

2144

3215

4287

5359

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

284

568

852

1136

1420

<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:

0.164

Hom.:

4202

Bravo

AF:

0.184

Asia WGS

AF:

0.110

AC:

385

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

1.8

(source)

DANN

Benign

0.57

PhyloP100

-0.28

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