Genetic Variant LINC02935:n.420-4906A>C (chr10-112936173-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 ENST00000428766.3(LINC02935):n.420-4906A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.224 in 152,064 control chromosomes in the GnomAD database, including 4,235 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 0.22 ( 4235 hom., cov: 31)

Consequence

LINC02935
ENST00000428766.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.08

Publications

8 publications found

Variant links:

Genes affected

LINC02935 (HGNC:55939): (long intergenic non-protein coding RNA 2935)

LINC02935 links:

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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 (AMR) allele frequency at 95% confidence interval = 0.28 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
LINC02935	ENST00000428766.3 link	n.420-4906A>C	intron_variant	Intron 3 of 7	5
LINC02935	ENST00000785198.1 link	n.418-8086A>C	intron_variant	Intron 3 of 3
LINC02935	ENST00000785199.1 link	n.189-4906A>C	intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.224

AC:

34006

AN:

151946

Hom.:

4230

Cov.:

show subpopulations

Gnomad AFR

AF:

0.111

Gnomad AMI

AF:

0.370

Gnomad AMR

AF:

0.287

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.0630

Gnomad SAS

AF:

0.214

Gnomad FIN

AF:

0.264

Gnomad MID

AF:

0.231

Gnomad NFE

AF:

0.283

Gnomad OTH

AF:

0.237

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

GnomAD4 genome

AF:

0.224

AC:

34029

AN:

152064

Hom.:

4235

Cov.:

AF XY:

0.222

AC XY:

16527

AN XY:

74334

show subpopulations

African (AFR)

AF:

0.111

AC:

4608

AN:

41526

American (AMR)

AF:

0.287

AC:

4377

AN:

15260

Ashkenazi Jewish (ASJ)

AF:

0.219

AC:

760

AN:

3470

East Asian (EAS)

AF:

0.0633

AC:

328

AN:

5180

South Asian (SAS)

AF:

0.214

AC:

1033

AN:

4818

European-Finnish (FIN)

AF:

0.264

AC:

2784

AN:

10548

Middle Eastern (MID)

AF:

0.235

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.283

AC:

19233

AN:

67952

Other (OTH)

AF:

0.237

AC:

500

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1307

2613

3920

5226

6533

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

356

712

1068

1424

1780

<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:

0.226

Hom.:

2253

Bravo

AF:

0.218

Asia WGS

AF:

0.189

AC:

657

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

0.96

(source)

DANN

Benign

0.77

PhyloP100

-2.1

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