Genetic Variant LINC02033:n.104-72G>A (chr3-36821489-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000623207.1(LINC02033):n.104-72G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 151,948 control chromosomes in the GnomAD database, including 10,793 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 0.37 ( 10791 hom., cov: 31)

Exomes 𝑓: 0.42 ( 2 hom. )

Consequence

LINC02033
ENST00000623207.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.184

Publications

20 publications found

Variant links:

Genes affected

LINC02033 (HGNC:52867): (long intergenic non-protein coding RNA 2033)

LINC02033 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=-0.92).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.442 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC02033	NR_147141.1 link	n.106-72G>A		intron_variant	Intron 1 of 1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
LINC02033	ENST00000623207.1 link	n.104-72G>A		intron_variant	Intron 1 of 1	2
LINC02033	ENST00000623312.1 link	n.-56G>A		upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.368

AC:

55847

AN:

151802

Hom.:

10778

Cov.:

show subpopulations

Gnomad AFR

AF:

0.447

Gnomad AMI

AF:

0.355

Gnomad AMR

AF:

0.366

Gnomad ASJ

AF:

0.297

Gnomad EAS

AF:

0.0605

Gnomad SAS

AF:

0.292

Gnomad FIN

AF:

0.300

Gnomad MID

AF:

0.313

Gnomad NFE

AF:

0.364

Gnomad OTH

AF:

0.346

GnomAD4 exome

AF:

0.423

AC:

AN:

Hom.:

AF XY:

0.571

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:

0.300

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.500

AC:

AN:

Other (OTH)

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

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:

0.368

AC:

55913

AN:

151922

Hom.:

10791

Cov.:

AF XY:

0.362

AC XY:

26877

AN XY:

74260

show subpopulations

African (AFR)

AF:

0.447

AC:

18521

AN:

41394

American (AMR)

AF:

0.366

AC:

5595

AN:

15272

Ashkenazi Jewish (ASJ)

AF:

0.297

AC:

1031

AN:

3472

East Asian (EAS)

AF:

0.0604

AC:

312

AN:

5162

South Asian (SAS)

AF:

0.293

AC:

1408

AN:

4812

European-Finnish (FIN)

AF:

0.300

AC:

3161

AN:

10536

Middle Eastern (MID)

AF:

0.296

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.364

AC:

24746

AN:

67954

Other (OTH)

AF:

0.344

AC:

728

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1751

3501

5252

7002

8753

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

532

1064

1596

2128

2660

<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:

0.364

Hom.:

35631

Bravo

AF:

0.375

Asia WGS

AF:

0.220

AC:

769

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.92

CADD

Benign

1.4

(source)

DANN

Benign

0.48

PhyloP100

-0.18

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