Genetic Variant ENST00000417542.1:n.199T>G (chr10-16283879-T-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000417542.1(LINC02654):n.199T>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 0.608 in 152,192 control chromosomes in the GnomAD database, including 31,228 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 0.61 ( 31145 hom., cov: 31)

Exomes 𝑓: 0.79 ( 83 hom. )

Consequence

LINC02654
ENST00000417542.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.818

Publications

2 publications found

Variant links:

Genes affected

LINC02654 (HGNC:54140): (long intergenic non-protein coding RNA 2654)

LINC02654 links:

ENSG00000295551 (HGNC:):

ENSG00000295551 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=-0.86).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.743 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02654	NR_184073.1 link	n.843T>G	non_coding_transcript_exon_variant	Exon 2 of 3
LINC02654	NR_184075.1 link	n.843T>G	non_coding_transcript_exon_variant	Exon 2 of 4
LINC02654	NR_184074.1 link	n.693+5130T>G	intron_variant	Intron 1 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02654	ENST00000417542.1 link	n.199T>G	non_coding_transcript_exon_variant	Exon 2 of 4	2
LINC02654	ENST00000434386.6 link	n.350T>G	non_coding_transcript_exon_variant	Exon 3 of 4	2
LINC02654	ENST00000654129.1 link	n.809T>G	non_coding_transcript_exon_variant	Exon 2 of 3

Frequencies

GnomAD3 genomes

AF:

0.608

AC:

92365

AN:

151812

Hom.:

31141

Cov.:

show subpopulations

Gnomad AFR

AF:

0.293

Gnomad AMI

AF:

0.692

Gnomad AMR

AF:

0.679

Gnomad ASJ

AF:

0.746

Gnomad EAS

AF:

0.606

Gnomad SAS

AF:

0.598

Gnomad FIN

AF:

0.781

Gnomad MID

AF:

0.677

Gnomad NFE

AF:

0.749

Gnomad OTH

AF:

0.633

GnomAD4 exome

AF:

0.792

AC:

206

AN:

260

Hom.:

Cov.:

AF XY:

0.762

AC XY:

125

AN XY:

164

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

1.00

AC:

AN:

East Asian (EAS)

AF:

0.500

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.773

AC:

102

AN:

132

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.855

AC:

AN:

110

Other (OTH)

AF:

0.500

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.576

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.608

AC:

92390

AN:

151932

Hom.:

31145

Cov.:

AF XY:

0.611

AC XY:

45360

AN XY:

74276

show subpopulations

African (AFR)

AF:

0.293

AC:

12126

AN:

41402

American (AMR)

AF:

0.679

AC:

10380

AN:

15278

Ashkenazi Jewish (ASJ)

AF:

0.746

AC:

2591

AN:

3472

East Asian (EAS)

AF:

0.606

AC:

3111

AN:

5134

South Asian (SAS)

AF:

0.599

AC:

2881

AN:

4812

European-Finnish (FIN)

AF:

0.781

AC:

8264

AN:

10578

Middle Eastern (MID)

AF:

0.670

AC:

197

AN:

294

European-Non Finnish (NFE)

AF:

0.749

AC:

50879

AN:

67946

Other (OTH)

AF:

0.632

AC:

1330

AN:

2104

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

1570

3140

4710

6280

7850

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

754

1508

2262

3016

3770

<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:

0.704

Hom.:

90402

Bravo

AF:

0.588

Asia WGS

AF:

0.597

AC:

2077

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.86

CADD

Benign

0.24

(source)

DANN

Benign

0.76

PhyloP100

-0.82

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

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over