Genetic Variant ENST00000598933.3:n.797A>C (chr16-85935285-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 ENST00000598933.3(LINC02132):n.797A>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 0.35 in 151,982 control chromosomes in the GnomAD database, including 10,498 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 0.35 ( 10498 hom., cov: 32)

Exomes 𝑓: 0.21 ( 0 hom. )

Consequence

LINC02132
ENST00000598933.3 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.06

Publications

4 publications found

Variant links:

Genes affected

LINC02132 (HGNC:52992): (long intergenic non-protein coding RNA 2132)

LINC02132 links:

ENSG00000285163 (HGNC:):

ENSG00000285163 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=-0.93).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.534 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02132	XR_001752391.2 link	n.697A>C		non_coding_transcript_exon_variant	Exon 2 of 2

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC02132	ENST00000598933.3 link	n.797A>C	non_coding_transcript_exon_variant	Exon 2 of 2	2
ENSG00000285163	ENST00000645383.1 link	n.393+3011T>G	intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646214.1 link	n.78-10131T>G	intron_variant	Intron 1 of 3
ENSG00000285163	ENST00000646986.2 link	n.-12T>G	upstream_gene_variant

Frequencies

GnomAD3 genomes

AF:

0.350

AC:

53166

AN:

151848

Hom.:

10466

Cov.:

show subpopulations

Gnomad AFR

AF:

0.539

Gnomad AMI

AF:

0.240

Gnomad AMR

AF:

0.275

Gnomad ASJ

AF:

0.245

Gnomad EAS

AF:

0.325

Gnomad SAS

AF:

0.301

Gnomad FIN

AF:

0.345

Gnomad MID

AF:

0.334

Gnomad NFE

AF:

0.267

Gnomad OTH

AF:

0.302

GnomAD4 exome

AF:

0.214

AC:

AN:

Hom.:

Cov.:

AF XY:

0.333

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)

AF:

0.500

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.333

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.575

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.350

AC:

53251

AN:

151968

Hom.:

10498

Cov.:

AF XY:

0.353

AC XY:

26207

AN XY:

74292

show subpopulations

African (AFR)

AF:

0.540

AC:

22343

AN:

41406

American (AMR)

AF:

0.275

AC:

4196

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.245

AC:

849

AN:

3460

East Asian (EAS)

AF:

0.325

AC:

1681

AN:

5168

South Asian (SAS)

AF:

0.302

AC:

1453

AN:

4814

European-Finnish (FIN)

AF:

0.345

AC:

3642

AN:

10562

Middle Eastern (MID)

AF:

0.336

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.267

AC:

18140

AN:

67978

Other (OTH)

AF:

0.299

AC:

631

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1677

3354

5031

6708

8385

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

500

1000

1500

2000

2500

<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:

0.333

Hom.:

1204

Bravo

AF:

0.357

Asia WGS

AF:

0.327

AC:

1137

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

2.6

(source)

DANN

Benign

0.20

PhyloP100

-1.1

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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