dbSNP rs13194504: LINC00533:n.240-13848C>T (chr6-28662914-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 ENST00000806405.1(LINC00533):n.240-13848C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.05 in 152,178 control chromosomes in the GnomAD database, including 320 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 0.050 ( 320 hom., cov: 31)

Consequence

LINC00533
ENST00000806405.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.232

Publications

38 publications found

Variant links:

Genes affected

LINC00533 (HGNC:18690): (long intergenic non-protein coding RNA 533)

LINC00533 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=-0.68).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0869 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00533	ENST00000806405.1 link	n.240-13848C>T	intron_variant	Intron 1 of 1
LINC00533	ENST00000806406.1 link	n.188-14263C>T	intron_variant	Intron 1 of 1
LINC00533	ENST00000806407.1 link	n.209-13858C>T	intron_variant	Intron 1 of 1

Frequencies

GnomAD3 genomes

AF:

0.0501

AC:

7612

AN:

152060

Hom.:

320

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0143

Gnomad AMI

AF:

0.126

Gnomad AMR

AF:

0.0199

Gnomad ASJ

AF:

0.0205

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000208

Gnomad FIN

AF:

0.0395

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0888

Gnomad OTH

AF:

0.0321

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

GnomAD4 genome

AF:

0.0500

AC:

7607

AN:

152178

Hom.:

320

Cov.:

AF XY:

0.0446

AC XY:

3322

AN XY:

74402

show subpopulations

African (AFR)

AF:

0.0142

AC:

591

AN:

41526

American (AMR)

AF:

0.0198

AC:

303

AN:

15270

Ashkenazi Jewish (ASJ)

AF:

0.0205

AC:

AN:

3470

East Asian (EAS)

AF:

0.00

AC:

AN:

5168

South Asian (SAS)

AF:

0.000208

AC:

AN:

4814

European-Finnish (FIN)

AF:

0.0395

AC:

419

AN:

10596

Middle Eastern (MID)

AF:

0.00340

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0888

AC:

6039

AN:

68016

Other (OTH)

AF:

0.0317

AC:

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

364

728

1093

1457

1821

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

184

276

368

460

<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:

0.0757

Hom.:

961

Bravo

AF:

0.0471

Asia WGS

AF:

0.00346

AC:

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

4.7

(source)

DANN

Benign

0.92

PhyloP100

0.23

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