dbSNP rs4555132: LINC00923:n.755+1649A>G (chr15-97396008-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000658446.1(LINC00923):n.639A>G variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 152,092 control chromosomes in the GnomAD database, including 4,165 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 0.23 ( 4165 hom., cov: 32)

Consequence

LINC00923
ENST00000658446.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.18

Publications

5 publications found

Variant links:

Genes affected

LINC00923 (HGNC:28088): (long intergenic non-protein coding RNA 923)

LINC00923 links:

LINC02253 (HGNC:53151): (long intergenic non-protein coding RNA 2253)

LINC02253 links:

LINC02254 (HGNC:53152): (long intergenic non-protein coding RNA 2254)

LINC02254 links:

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new If you want to explore the variant's impact on the transcript ENST00000658446.1, 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.

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 (NFE) allele frequency at 95% confidence interval = 0.25 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000658446.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
LINC02254	NR_120324.1	n.755+1649A>G	intron	N/A
LINC02253	NR_183853.1	n.293-15184T>C	intron	N/A
LINC02253	NR_183854.1	n.293-15184T>C	intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC00923	ENST00000558621.2	TSL:1	n.755+1649A>G	intron	N/A
LINC00923	ENST00000658446.1		n.639A>G	non_coding_transcript_exon	Exon 5 of 5
LINC00923	ENST00000740462.1		n.856A>G	non_coding_transcript_exon	Exon 5 of 5

Frequencies

GnomAD3 genomes

AF:

0.232

AC:

35193

AN:

151974

Hom.:

4160

Cov.:

show subpopulations

Gnomad AFR

AF:

0.205

Gnomad AMI

AF:

0.184

Gnomad AMR

AF:

0.247

Gnomad ASJ

AF:

0.209

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.172

Gnomad FIN

AF:

0.271

Gnomad MID

AF:

0.228

Gnomad NFE

AF:

0.253

Gnomad OTH

AF:

0.243

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

GnomAD4 genome

AF:

0.231

AC:

35203

AN:

152092

Hom.:

4165

Cov.:

AF XY:

0.230

AC XY:

17135

AN XY:

74346

show subpopulations

African (AFR)

AF:

0.204

AC:

8482

AN:

41506

American (AMR)

AF:

0.248

AC:

3784

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.209

AC:

724

AN:

3470

East Asian (EAS)

AF:

0.106

AC:

548

AN:

5158

South Asian (SAS)

AF:

0.171

AC:

823

AN:

4816

European-Finnish (FIN)

AF:

0.271

AC:

2873

AN:

10592

Middle Eastern (MID)

AF:

0.221

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.253

AC:

17229

AN:

67966

Other (OTH)

AF:

0.240

AC:

507

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

1369

2737

4106

5474

6843

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

362

724

1086

1448

1810

<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:

0.248

Hom.:

7990

Bravo

AF:

0.229

Asia WGS

AF:

0.125

AC:

435

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.14

(source)

DANN

Benign

0.51

PhyloP100

-2.2

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

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over