dbSNP rs67911569: LINC02997:n.520+33441G>A (chr5-67653730-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000503106.5(LINC02997):n.520+33441G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0871 in 152,130 control chromosomes in the GnomAD database, including 898 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 0.087 ( 898 hom., cov: 32)

Consequence

LINC02997
ENST00000503106.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Publications

1 publications found

Variant links:

Genes affected

LINC02997 (HGNC:56113): (long intergenic non-protein coding RNA 2997)

LINC02997 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=-0.98).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.294 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
LINC02997	ENST00000503106.5 link	n.520+33441G>A	intron_variant	Intron 3 of 3	4
LINC02997	ENST00000514368.2 link	n.125+33815G>A	intron_variant	Intron 1 of 5	3
LINC02997	ENST00000668508.1 link	n.248+33815G>A	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.0869

AC:

13217

AN:

152012

Hom.:

892

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0290

Gnomad AMI

AF:

0.0197

Gnomad AMR

AF:

0.169

Gnomad ASJ

AF:

0.0557

Gnomad EAS

AF:

0.307

Gnomad SAS

AF:

0.0818

Gnomad FIN

AF:

0.0956

Gnomad MID

AF:

0.0253

Gnomad NFE

AF:

0.0889

Gnomad OTH

AF:

0.0916

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

GnomAD4 genome

AF:

0.0871

AC:

13244

AN:

152130

Hom.:

898

Cov.:

AF XY:

0.0895

AC XY:

6660

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.0293

AC:

1217

AN:

41540

American (AMR)

AF:

0.169

AC:

2580

AN:

15256

Ashkenazi Jewish (ASJ)

AF:

0.0557

AC:

193

AN:

3468

East Asian (EAS)

AF:

0.306

AC:

1582

AN:

5162

South Asian (SAS)

AF:

0.0814

AC:

393

AN:

4826

European-Finnish (FIN)

AF:

0.0956

AC:

1012

AN:

10586

Middle Eastern (MID)

AF:

0.0272

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0889

AC:

6041

AN:

67978

Other (OTH)

AF:

0.0949

AC:

200

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

586

1171

1757

2342

2928

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

146

292

438

584

730

<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:

0.0781

Hom.:

154

Bravo

AF:

0.0914

Asia WGS

AF:

0.175

AC:

608

AN:

3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.12

(source)

DANN

Benign

0.57

PhyloP100

-1.5

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