dbSNP rs2568958: LINC02796:n.236+16028G>A (chr1-72299433-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is The variant received -12 classification points (ACMG Germline Pathogenicity v2019). BA1BP4_Strong

The XR_001737670.2(LOC105378797):n.472+16028G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. Note: XR_001737670.2 is not a MANE Select or MANE Plus Clinical transcript for LOC105378797; the reported annotation may differ from that of the MANE-designated reference transcript for this gene. The variant allele was found at a cumulative frequency of 0.625 (AC=94,918) in the gnomAD database across 151,952 control chromosomes, including 30,286 homozygotes. The grpmax filtering allele frequency (95% CI) is 0.901. In-silico predictor (BayesDel (noAF)) classifies this variant as likely benign. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.62 ( 30286 hom., cov: 31)

Consequence

LOC105378797
XR_001737670.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.388

Publications

152 publications found

Variant links:

Genes affected

LINC02796 (HGNC:27918): (long intergenic non-protein coding RNA 2796)

LINC02796 links:

LOC105378797 (HGNC:):

LOC105378797 links:

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new If you want to explore the variant's impact on the transcript XR_001737670.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

Classification according to ACMG Germline Pathogenicity v2019

Classification was made for transcript

Our verdict: Benign. The variant received -12 points.

BP4

Computational evidence supports benign — no pathogenic computational or splicing signal (BP4); No splicing predictor data available.; Germline computational verdict: benign (Strong).

BA1

GnomAD effective popmax AF >5% — BA1 stand-alone benign; GnomAD reliable popmax AF = 0.9010 — exceeds 5%% threshold (BA1 applied)

Variant Effect in Transcripts

Automated classification analysis was done for transcript: ENST00000715640.2. You can select a different transcript below to see updated classification assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LINC02796	ENST00000715640.2	n.236+16028G>A	intron	N/A
LINC02796	ENST00000715641.1	n.227+16028G>A	intron	N/A
LINC02796	ENST00000715642.1	n.153+16028G>A	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.625

AC:

94872

AN:

151834

Hom.:

30272

Cov.:

show subpopulations

Gnomad AFR

AF:

0.541

Gnomad AMI

AF:

0.554

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.735

Gnomad EAS

AF:

0.924

Gnomad SAS

AF:

0.667

Gnomad FIN

AF:

0.648

Gnomad MID

AF:

0.722

Gnomad NFE

AF:

0.623

Gnomad OTH

AF:

0.640

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

GnomAD4 genome

AF:

0.625

AC:

94918

AN:

151952

Hom.:

30286

Cov.:

AF XY:

0.631

AC XY:

46868

AN XY:

74288

show subpopulations

African (AFR)

AF:

0.540

AC:

22364

AN:

41424

American (AMR)

AF:

0.708

AC:

10813

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.735

AC:

2550

AN:

3468

East Asian (EAS)

AF:

0.923

AC:

4724

AN:

5118

South Asian (SAS)

AF:

0.668

AC:

3218

AN:

4816

European-Finnish (FIN)

AF:

0.648

AC:

6856

AN:

10576

Middle Eastern (MID)

AF:

0.731

AC:

215

AN:

294

European-Non Finnish (NFE)

AF:

0.623

AC:

42317

AN:

67966

Other (OTH)

AF:

0.643

AC:

1357

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1752

3504

5255

7007

8759

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

784

1568

2352

3136

3920

<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:

0.631

Hom.:

131084

Bravo

AF:

0.628

Asia WGS

AF:

0.753

AC:

2614

AN:

3478

Local populations

ToMMo 61KJPN (+60KJPN MNV)

AF:

0.930

AC:

114193

AN:

122826

Turkish Variome

AF:

0.712

AC:

1100

AN:

1544

Hom.:

395

WBBC (Westlake BioBank for Chinese) pilot

AF:

0.919

AC:

8233

AN:

8960

Hom.:

3780

ABraOM SABE-WGS-1171

AF:

0.670

AC:

1568

AN:

2342

Hom.:

538

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

0.14

(source)

DANN

Benign

0.31

PhyloP100

-0.39

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

Classification according to ACMG Germline Pathogenicity v2019

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Local populations

ClinVar

Computational scores

Splicing

Publications

Other links and lift over