Genetic Variant LINC02934:n.786+22023A>G (chr2-65921332-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 ENST00000606978.5(LINC02934):n.786+22023A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.616 in 152,078 control chromosomes in the GnomAD database, including 30,840 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 0.62 ( 30840 hom., cov: 32)

Consequence

LINC02934
ENST00000606978.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.197

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=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.855 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02934	NR_187140.1 link	n.61-606A>G		intron_variant	Intron 1 of 5
LINC02934	NR_187141.1 link	n.61-50216A>G		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02934	ENST00000606978.5 link	n.786+22023A>G		intron_variant	Intron 7 of 9	5

Frequencies

GnomAD3 genomes

AF:

0.615

AC:

93523

AN:

151960

Hom.:

30785

Cov.:

show subpopulations

Gnomad AFR

AF:

0.863

Gnomad AMI

AF:

0.332

Gnomad AMR

AF:

0.585

Gnomad ASJ

AF:

0.462

Gnomad EAS

AF:

0.723

Gnomad SAS

AF:

0.631

Gnomad FIN

AF:

0.553

Gnomad MID

AF:

0.497

Gnomad NFE

AF:

0.486

Gnomad OTH

AF:

0.551

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

GnomAD4 genome

AF:

0.616

AC:

93639

AN:

152078

Hom.:

30840

Cov.:

AF XY:

0.620

AC XY:

46112

AN XY:

74324

show subpopulations

African (AFR)

AF:

0.863

AC:

35818

AN:

41516

American (AMR)

AF:

0.585

AC:

8938

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.462

AC:

1602

AN:

3468

East Asian (EAS)

AF:

0.723

AC:

3738

AN:

5168

South Asian (SAS)

AF:

0.631

AC:

3041

AN:

4816

European-Finnish (FIN)

AF:

0.553

AC:

5836

AN:

10558

Middle Eastern (MID)

AF:

0.507

AC:

149

AN:

294

European-Non Finnish (NFE)

AF:

0.486

AC:

33050

AN:

67962

Other (OTH)

AF:

0.552

AC:

1165

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1656

3312

4967

6623

8279

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

750

1500

2250

3000

3750

<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:

0.528

Hom.:

71060

Bravo

AF:

0.626

Asia WGS

AF:

0.683

AC:

2374

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.9

(source)

DANN

Benign

0.55

PhyloP100

-0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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