dbSNP rs2969344: LINC01117:n.398+20066G>A (chr2-176517861-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 ENST00000652995.1(LINC01117):n.398+20066G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0957 in 152,186 control chromosomes in the GnomAD database, including 779 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 0.096 ( 779 hom., cov: 32)

Consequence

LINC01117
ENST00000652995.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.336

Publications

4 publications found

Variant links:

Genes affected

LINC01117 (HGNC:49260): (long intergenic non-protein coding RNA 1117)

LINC01117 links:

ENSG00000306098 (HGNC:):

ENSG00000306098 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=-0.75).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.152 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC01117	ENST00000652995.1 link	n.398+20066G>A	intron_variant	Intron 2 of 3
LINC01117	ENST00000814385.1 link	n.185+22291G>A	intron_variant	Intron 2 of 4
LINC01117	ENST00000814386.1 link	n.245+22291G>A	intron_variant	Intron 2 of 6

Frequencies

GnomAD3 genomes

AF:

0.0957

AC:

14553

AN:

152068

Hom.:

777

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0585

Gnomad AMI

AF:

0.0417

Gnomad AMR

AF:

0.0937

Gnomad ASJ

AF:

0.0919

Gnomad EAS

AF:

0.0266

Gnomad SAS

AF:

0.161

Gnomad FIN

AF:

0.100

Gnomad MID

AF:

0.0918

Gnomad NFE

AF:

0.119

Gnomad OTH

AF:

0.110

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

GnomAD4 genome

AF:

0.0957

AC:

14569

AN:

152186

Hom.:

779

Cov.:

AF XY:

0.0950

AC XY:

7071

AN XY:

74398

show subpopulations

African (AFR)

AF:

0.0586

AC:

2435

AN:

41522

American (AMR)

AF:

0.0937

AC:

1432

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.0919

AC:

319

AN:

3470

East Asian (EAS)

AF:

0.0267

AC:

138

AN:

5176

South Asian (SAS)

AF:

0.162

AC:

779

AN:

4812

European-Finnish (FIN)

AF:

0.100

AC:

1059

AN:

10590

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.119

AC:

8112

AN:

68018

Other (OTH)

AF:

0.109

AC:

230

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

670

1340

2009

2679

3349

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

166

332

498

664

830

<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:

0.107

Hom.:

2037

Bravo

AF:

0.0916

Asia WGS

AF:

0.107

AC:

372

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

5.1

(source)

DANN

Benign

0.74

PhyloP100

0.34

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