Genetic Variant LINC01828:n.88+5466T>C (chr2-67218961-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000445514.1(LINC01828):n.88+5466T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0915 in 152,280 control chromosomes in the GnomAD database, including 861 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 0.091 ( 861 hom., cov: 32)

Consequence

LINC01828
ENST00000445514.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.664

Publications

2 publications found

Variant links:

Genes affected

LINC01828 (HGNC:52634): (long intergenic non-protein coding RNA 1828)

LINC01828 links:

LINC01829 (HGNC:52635): (long intergenic non-protein coding RNA 1829)

LINC01829 links:

LOC101927661 (HGNC:):

LOC101927661 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000445514.1, 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=-0.93).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000445514.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01828	NR_110564.1		n.111-46036T>C		intron	N/A
	LOC101927661	NR_110568.1		n.88+5466T>C		intron	N/A

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
LINC01828	ENST00000445514.1	TSL:4	n.88+5466T>C	intron	N/A
LINC01828	ENST00000452716.5	TSL:5	n.111-46036T>C	intron	N/A
LINC01828	ENST00000594329.5	TSL:5	n.452-10438T>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.0916

AC:

13940

AN:

152164

Hom.:

863

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0244

Gnomad AMI

AF:

0.0789

Gnomad AMR

AF:

0.0784

Gnomad ASJ

AF:

0.196

Gnomad EAS

AF:

0.00231

Gnomad SAS

AF:

0.171

Gnomad FIN

AF:

0.0920

Gnomad MID

AF:

0.225

Gnomad NFE

AF:

0.130

Gnomad OTH

AF:

0.119

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

GnomAD4 genome

AF:

0.0915

AC:

13929

AN:

152280

Hom.:

861

Cov.:

AF XY:

0.0899

AC XY:

6693

AN XY:

74460

show subpopulations

African (AFR)

AF:

0.0243

AC:

1012

AN:

41564

American (AMR)

AF:

0.0783

AC:

1197

AN:

15294

Ashkenazi Jewish (ASJ)

AF:

0.196

AC:

680

AN:

3468

East Asian (EAS)

AF:

0.00212

AC:

AN:

5182

South Asian (SAS)

AF:

0.170

AC:

822

AN:

4822

European-Finnish (FIN)

AF:

0.0920

AC:

977

AN:

10614

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.130

AC:

8844

AN:

68018

Other (OTH)

AF:

0.117

AC:

247

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

648

1296

1943

2591

3239

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

176

352

528

704

880

<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:

0.111

Hom.:

973

Bravo

AF:

0.0850

Asia WGS

AF:

0.0660

AC:

231

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

1.6

(source)

DANN

Benign

0.48

PhyloP100

-0.66

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