Genetic Variant LINC00511:n.74-206A>G (chr17-72428504-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000457958.7(LINC00511):n.74-206A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.66 in 152,156 control chromosomes in the GnomAD database, including 33,828 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 0.66 ( 33828 hom., cov: 33)

Failed GnomAD Quality Control

Consequence

LINC00511
ENST00000457958.7 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.83

Publications

3 publications found

Variant links:

Genes affected

LINC00511 (HGNC:43564): (long intergenic non-protein coding RNA 511)

LINC00511 links:

ENSG00000263680 (HGNC:):

ENSG00000263680 links:

LINC00673 (HGNC:44354): (long intergenic non-protein coding RNA 673) This gene produces a long non-protein coding RNA that is involved in the regulation of gene expression during tumor progression. This transcript can promote cell proliferation in gastric cancer through interaction with enhancer of zeste 2 and other epigenetic suppressors of gene expression, thereby downregulating target genes including Kruppel like factors 2 and 4. This transcript may also act as a tumor suppressor by promoting interaction between protein tyrosine phosphatase, non-receptor type 11 (Ptpn11) and ubiquitin ligase, resulting in degradation of Ptpn11 and lowered oncogenic signalling. Naturally-occurring variation at this locus results in the formation of a binding site for miR-1231, which negatively regulates activity of this transcript. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Dec 2017]

LINC00673 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=-0.94).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.78 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00673	NR_036488.1 link	n.700-206A>G	intron_variant	Intron 2 of 3
LINC00673	NR_137280.2 link	n.603-206A>G	intron_variant	Intron 1 of 3
LINC00673	NR_137281.2 link	n.700-206A>G	intron_variant	Intron 2 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC00511	ENST00000457958.7 link	n.74-206A>G	intron_variant	Intron 1 of 2	1
ENSG00000263680	ENST00000577281.2 link	n.485T>C	non_coding_transcript_exon_variant	Exon 2 of 2	3
LINC00511	ENST00000453722.6 link	n.700-206A>G	intron_variant	Intron 2 of 4	2

Frequencies

GnomAD3 genomes

AF:

0.660

AC:

100310

AN:

152038

Hom.:

33790

Cov.:

show subpopulations

Gnomad AFR

AF:

0.787

Gnomad AMI

AF:

0.754

Gnomad AMR

AF:

0.522

Gnomad ASJ

AF:

0.608

Gnomad EAS

AF:

0.801

Gnomad SAS

AF:

0.479

Gnomad FIN

AF:

0.677

Gnomad MID

AF:

0.630

Gnomad NFE

AF:

0.615

Gnomad OTH

AF:

0.633

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AC:

AN:

Hom.:

Cov.:

AC XY:

AN XY:

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)

AC:

AN:

Other (OTH)

AC:

AN:

GnomAD4 genome

AF:

0.660

AC:

100397

AN:

152156

Hom.:

33828

Cov.:

AF XY:

0.659

AC XY:

49028

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.787

AC:

32665

AN:

41522

American (AMR)

AF:

0.522

AC:

7979

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.608

AC:

2111

AN:

3470

East Asian (EAS)

AF:

0.800

AC:

4142

AN:

5178

South Asian (SAS)

AF:

0.479

AC:

2308

AN:

4818

European-Finnish (FIN)

AF:

0.677

AC:

7164

AN:

10578

Middle Eastern (MID)

AF:

0.636

AC:

187

AN:

294

European-Non Finnish (NFE)

AF:

0.615

AC:

41820

AN:

67992

Other (OTH)

AF:

0.633

AC:

1333

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1729

3457

5186

6914

8643

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

790

1580

2370

3160

3950

<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:

0.613

Hom.:

16637

Bravo

AF:

0.658

Asia WGS

AF:

0.602

AC:

2091

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.94

CADD

Benign

0.0080

(source)

DANN

Benign

0.61

PhyloP100

-1.8

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