Genetic Variant LINC02177:n.90+32495G>T (chr16-9319747-G-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000784364.1(LINC02177):n.90+32495G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.415 in 152,114 control chromosomes in the GnomAD database, including 13,734 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 0.41 ( 13734 hom., cov: 32)

Consequence

LINC02177
ENST00000784364.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.113

Publications

0 publications found

Variant links:

Genes affected

LINC02177 (HGNC:53039): (long intergenic non-protein coding RNA 2177)

LINC02177 links:

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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=-0.82).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC02177	ENST00000784364.1 link	n.90+32495G>T	intron_variant	Intron 1 of 2
LINC02177	ENST00000784365.1 link	n.85+32495G>T	intron_variant	Intron 1 of 3
LINC02177	ENST00000784366.1 link	n.69+32495G>T	intron_variant	Intron 1 of 4

Frequencies

GnomAD3 genomes

AF:

0.415

AC:

63055

AN:

151996

Hom.:

13739

Cov.:

show subpopulations

Gnomad AFR

AF:

0.308

Gnomad AMI

AF:

0.676

Gnomad AMR

AF:

0.371

Gnomad ASJ

AF:

0.428

Gnomad EAS

AF:

0.211

Gnomad SAS

AF:

0.443

Gnomad FIN

AF:

0.523

Gnomad MID

AF:

0.456

Gnomad NFE

AF:

0.482

Gnomad OTH

AF:

0.412

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

GnomAD4 genome

AF:

0.415

AC:

63060

AN:

152114

Hom.:

13734

Cov.:

AF XY:

0.414

AC XY:

30752

AN XY:

74338

show subpopulations

African (AFR)

AF:

0.307

AC:

12754

AN:

41504

American (AMR)

AF:

0.371

AC:

5668

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.428

AC:

1486

AN:

3470

East Asian (EAS)

AF:

0.211

AC:

1091

AN:

5170

South Asian (SAS)

AF:

0.444

AC:

2135

AN:

4810

European-Finnish (FIN)

AF:

0.523

AC:

5530

AN:

10568

Middle Eastern (MID)

AF:

0.456

AC:

134

AN:

294

European-Non Finnish (NFE)

AF:

0.482

AC:

32782

AN:

67994

Other (OTH)

AF:

0.410

AC:

866

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1849

3697

5546

7394

9243

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

598

1196

1794

2392

2990

<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:

0.454

Hom.:

3395

Bravo

AF:

0.397

Asia WGS

AF:

0.317

AC:

1105

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.82

CADD

Benign

0.44

(source)

DANN

Benign

0.63

PhyloP100

-0.11

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