Genetic Variant LINC02934:n.668+23714A>C (chr2-65778497-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 ENST00000606978.5(LINC02934):n.668+23714A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.176 in 152,094 control chromosomes in the GnomAD database, including 3,880 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 ( 3880 hom., cov: 33)

Consequence

LINC02934
ENST00000606978.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.121

Publications

1 publications found

Variant links:

Genes affected

LINC02934 (HGNC:55913): (long intergenic non-protein coding RNA 2934)

LINC02934 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=-0.9).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606978.5 link	n.668+23714A>C		intron_variant	Intron 6 of 9	5
LINC02934	ENST00000822281.1 link	n.333-9629A>C		intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.176

AC:

26770

AN:

151976

Hom.:

3871

Cov.:

show subpopulations

Gnomad AFR

AF:

0.384

Gnomad AMI

AF:

0.0614

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.0810

Gnomad EAS

AF:

0.369

Gnomad SAS

AF:

0.183

Gnomad FIN

AF:

0.0887

Gnomad MID

AF:

0.117

Gnomad NFE

AF:

0.0563

Gnomad OTH

AF:

0.151

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

GnomAD4 genome

AF:

0.176

AC:

26827

AN:

152094

Hom.:

3880

Cov.:

AF XY:

0.178

AC XY:

13242

AN XY:

74366

show subpopulations

African (AFR)

AF:

0.384

AC:

15922

AN:

41450

American (AMR)

AF:

0.174

AC:

2663

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.0810

AC:

281

AN:

3468

East Asian (EAS)

AF:

0.368

AC:

1905

AN:

5174

South Asian (SAS)

AF:

0.182

AC:

877

AN:

4814

European-Finnish (FIN)

AF:

0.0887

AC:

941

AN:

10608

Middle Eastern (MID)

AF:

0.122

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0563

AC:

3824

AN:

67974

Other (OTH)

AF:

0.153

AC:

322

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

988

1977

2965

3954

4942

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

266

532

798

1064

1330

<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:

0.140

Hom.:

1317

Bravo

AF:

0.190

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

1.8

(source)

DANN

Benign

0.58

PhyloP100

0.12

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