Genetic Variant LINC01697:n.449G>A (chr21-28102898-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 ENST00000458316.2(LINC01697):n.449G>A 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 0.23 in 151,856 control chromosomes in the GnomAD database, including 5,393 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 ( 5393 hom., cov: 32)

Exomes 𝑓: 0.20 ( 0 hom. )

Consequence

LINC01697
ENST00000458316.2 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.343

Publications

3 publications found

Variant links:

Genes affected

LINC01697 (HGNC:52485): (long intergenic non-protein coding RNA 1697)

LINC01697 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=-0.91).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.436 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01697	NR_126011.1 link	n.522G>A		non_coding_transcript_exon_variant	Exon 3 of 3
LINC01697	NR_126010.1 link	n.344+129G>A		intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01697	ENST00000458316.2 link	n.449G>A	non_coding_transcript_exon_variant	Exon 2 of 2	1
LINC01697	ENST00000436878.2 link	n.686G>A	non_coding_transcript_exon_variant	Exon 3 of 3	2
LINC01697	ENST00000631186.1 link	n.495G>A	non_coding_transcript_exon_variant	Exon 2 of 2	5

Frequencies

GnomAD3 genomes

AF:

0.230

AC:

34870

AN:

151728

Hom.:

5379

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.116

Gnomad AMR

AF:

0.174

Gnomad ASJ

AF:

0.0860

Gnomad EAS

AF:

0.450

Gnomad SAS

AF:

0.176

Gnomad FIN

AF:

0.118

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.139

Gnomad OTH

AF:

0.215

GnomAD4 exome

AF:

0.200

AC:

AN:

Hom.:

Cov.:

AF XY:

0.250

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.250

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.775

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.230

AC:

34923

AN:

151846

Hom.:

5393

Cov.:

AF XY:

0.229

AC XY:

16964

AN XY:

74208

show subpopulations

African (AFR)

AF:

0.424

AC:

17527

AN:

41326

American (AMR)

AF:

0.174

AC:

2652

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.0860

AC:

298

AN:

3466

East Asian (EAS)

AF:

0.451

AC:

2312

AN:

5124

South Asian (SAS)

AF:

0.175

AC:

844

AN:

4814

European-Finnish (FIN)

AF:

0.118

AC:

1248

AN:

10576

Middle Eastern (MID)

AF:

0.197

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.139

AC:

9427

AN:

67950

Other (OTH)

AF:

0.214

AC:

451

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1236

2472

3707

4943

6179

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

354

708

1062

1416

1770

<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:

0.168

Hom.:

1449

Bravo

AF:

0.244

Asia WGS

AF:

0.294

AC:

1022

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

1.3

(source)

DANN

Benign

0.21

PhyloP100

-0.34

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