Genetic Variant LINC01497:n.90G>C (chr17-69961633-G-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000420427.3(LINC01497):n.90G>C 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 0.763 in 152,414 control chromosomes in the GnomAD database, including 45,226 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 0.76 ( 45155 hom., cov: 42)

Exomes 𝑓: 0.87 ( 71 hom. )

Consequence

LINC01497
ENST00000420427.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.287

Publications

7 publications found

Variant links:

Genes affected

LINC01497 (HGNC:51163): (long intergenic non-protein coding RNA 1497)

LINC01497 links:

ENSG00000295979 (HGNC:):

ENSG00000295979 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=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.937 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01497	NR_110874.1 link	n.-74G>C		upstream_gene_variant
LINC01497	NR_110875.1 link	n.-74G>C		upstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01497	ENST00000420427.3 link	n.90G>C	non_coding_transcript_exon_variant	Exon 1 of 5	3
LINC01497	ENST00000455460.7 link	n.90G>C	non_coding_transcript_exon_variant	Exon 1 of 5	3
LINC01497	ENST00000654068.2 link	n.402G>C	non_coding_transcript_exon_variant	Exon 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.763

AC:

116054

AN:

152112

Hom.:

45092

Cov.:

show subpopulations

Gnomad AFR

AF:

0.936

Gnomad AMI

AF:

0.782

Gnomad AMR

AF:

0.753

Gnomad ASJ

AF:

0.702

Gnomad EAS

AF:

0.959

Gnomad SAS

AF:

0.843

Gnomad FIN

AF:

0.670

Gnomad MID

AF:

0.794

Gnomad NFE

AF:

0.657

Gnomad OTH

AF:

0.739

GnomAD4 exome

AF:

0.870

AC:

160

AN:

184

Hom.:

AF XY:

0.861

AC XY:

124

AN XY:

144

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.750

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.857

AC:

120

AN:

140

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.639

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:

0.763

AC:

116176

AN:

152230

Hom.:

45155

Cov.:

AF XY:

0.766

AC XY:

57013

AN XY:

74432

show subpopulations

African (AFR)

AF:

0.936

AC:

38922

AN:

41592

American (AMR)

AF:

0.753

AC:

11514

AN:

15296

Ashkenazi Jewish (ASJ)

AF:

0.702

AC:

2437

AN:

3472

East Asian (EAS)

AF:

0.959

AC:

4977

AN:

5188

South Asian (SAS)

AF:

0.843

AC:

4076

AN:

4834

European-Finnish (FIN)

AF:

0.670

AC:

7091

AN:

10586

Middle Eastern (MID)

AF:

0.793

AC:

233

AN:

294

European-Non Finnish (NFE)

AF:

0.657

AC:

44644

AN:

67942

Other (OTH)

AF:

0.742

AC:

1569

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.584

Heterozygous variant carriers

851

1702

2554

3405

4256

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

852

1704

2556

3408

4260

<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:

0.579

Hom.:

1414

Bravo

AF:

0.791

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

2.0

(source)

DANN

Benign

0.41

PhyloP100

-0.29

Mutation Taster

=100/0

polymorphism

(source)

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