Genetic Variant LINC01915:n.511+54222G>A (chr18-24589283-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 ENST00000664008.1(LINC01915):n.511+54222G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0342 in 152,214 control chromosomes in the GnomAD database, including 225 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 0.034 ( 225 hom., cov: 32)

Consequence

LINC01915
ENST00000664008.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.632

Publications

0 publications found

Variant links:

Genes affected

LINC01915 (HGNC:52734): (long intergenic non-protein coding RNA 1915)

LINC01915 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=-0.92).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.0763 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC01915	ENST00000664008.1 link	n.511+54222G>A		intron_variant	Intron 1 of 1
LINC01915	ENST00000762860.1 link	n.143-29012G>A		intron_variant	Intron 1 of 6

Frequencies

GnomAD3 genomes

AF:

0.0342

AC:

5199

AN:

152096

Hom.:

224

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0741

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.0802

Gnomad ASJ

AF:

0.00490

Gnomad EAS

AF:

0.0731

Gnomad SAS

AF:

0.0568

Gnomad FIN

AF:

0.00160

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.00237

Gnomad OTH

AF:

0.0277

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

GnomAD4 genome

AF:

0.0342

AC:

5207

AN:

152214

Hom.:

225

Cov.:

AF XY:

0.0361

AC XY:

2685

AN XY:

74420

show subpopulations

African (AFR)

AF:

0.0741

AC:

3077

AN:

41514

American (AMR)

AF:

0.0800

AC:

1223

AN:

15292

Ashkenazi Jewish (ASJ)

AF:

0.00490

AC:

AN:

3470

East Asian (EAS)

AF:

0.0733

AC:

379

AN:

5172

South Asian (SAS)

AF:

0.0565

AC:

272

AN:

4818

European-Finnish (FIN)

AF:

0.00160

AC:

AN:

10602

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.00237

AC:

161

AN:

68026

Other (OTH)

AF:

0.0284

AC:

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

248

496

745

993

1241

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

104

156

208

260

<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:

0.0201

Hom.:

Bravo

AF:

0.0412

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

0.58

(source)

DANN

Benign

0.28

PhyloP100

-0.63

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