dbSNP rs2860851: LINC02934:n.633+13324T>C (chr2-65705283-T-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.633+13324T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0514 in 152,130 control chromosomes in the GnomAD database, including 372 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 0.051 ( 372 hom., cov: 32)

Consequence

LINC02934
ENST00000606978.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0200

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=-0.92).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.115 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
LINC02934	ENST00000606978.5 link	n.633+13324T>C	intron_variant	Intron 5 of 9	5
LINC02934	ENST00000822260.1 link	n.545+13324T>C	intron_variant	Intron 4 of 4
LINC02934	ENST00000822283.1 link	n.216+13324T>C	intron_variant	Intron 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.0514

AC:

7807

AN:

152012

Hom.:

372

Cov.:

show subpopulations

Gnomad AFR

AF:

0.112

Gnomad AMI

AF:

0.00219

Gnomad AMR

AF:

0.0577

Gnomad ASJ

AF:

0.00865

Gnomad EAS

AF:

0.0990

Gnomad SAS

AF:

0.123

Gnomad FIN

AF:

0.0113

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0138

Gnomad OTH

AF:

0.0464

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

GnomAD4 genome

AF:

0.0514

AC:

7814

AN:

152130

Hom.:

372

Cov.:

AF XY:

0.0520

AC XY:

3868

AN XY:

74400

show subpopulations

African (AFR)

AF:

0.112

AC:

4631

AN:

41486

American (AMR)

AF:

0.0577

AC:

882

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.00865

AC:

AN:

3470

East Asian (EAS)

AF:

0.0983

AC:

509

AN:

5180

South Asian (SAS)

AF:

0.124

AC:

595

AN:

4816

European-Finnish (FIN)

AF:

0.0113

AC:

120

AN:

10608

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0138

AC:

939

AN:

67972

Other (OTH)

AF:

0.0464

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

351

703

1054

1406

1757

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

188

282

376

470

<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:

0.0271

Hom.:

Bravo

AF:

0.0572

Asia WGS

AF:

0.123

AC:

429

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.77

(source)

DANN

Benign

0.55

PhyloP100

-0.020

Mutation Taster

=100/0

polymorphism

(source)

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