dbSNP rs10519469: LINC00499:n.486-6921A>G (chr4-138514635-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000653577.1(LINC00499):n.486-6921A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.083 in 152,254 control chromosomes in the GnomAD database, including 585 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 0.083 ( 585 hom., cov: 32)

Consequence

LINC00499
ENST00000653577.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.491

Publications

3 publications found

Variant links:

Genes affected

LINC00499 (HGNC:43436): (long intergenic non-protein coding RNA 499)

LINC00499 links:

ENSG00000297834 (HGNC:):

ENSG00000297834 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=-0.91).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.165 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank
LINC00499	ENST00000653577.1 link	n.486-6921A>G	intron_variant	Intron 4 of 5
LINC00499	ENST00000655654.1 link	n.597-6921A>G	intron_variant	Intron 4 of 5
LINC00499	ENST00000656561.1 link	n.468-6924A>G	intron_variant	Intron 3 of 4

Frequencies

GnomAD3 genomes

AF:

0.0829

AC:

12612

AN:

152136

Hom.:

585

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0487

Gnomad AMI

AF:

0.0548

Gnomad AMR

AF:

0.0931

Gnomad ASJ

AF:

0.0524

Gnomad EAS

AF:

0.0580

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.130

Gnomad MID

AF:

0.0696

Gnomad NFE

AF:

0.0917

Gnomad OTH

AF:

0.0740

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

GnomAD4 genome

AF:

0.0830

AC:

12630

AN:

152254

Hom.:

585

Cov.:

AF XY:

0.0841

AC XY:

6257

AN XY:

74442

show subpopulations

African (AFR)

AF:

0.0487

AC:

2023

AN:

41572

American (AMR)

AF:

0.0934

AC:

1427

AN:

15276

Ashkenazi Jewish (ASJ)

AF:

0.0524

AC:

182

AN:

3472

East Asian (EAS)

AF:

0.0583

AC:

302

AN:

5178

South Asian (SAS)

AF:

0.175

AC:

842

AN:

4820

European-Finnish (FIN)

AF:

0.130

AC:

1381

AN:

10604

Middle Eastern (MID)

AF:

0.0646

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0918

AC:

6240

AN:

68010

Other (OTH)

AF:

0.0775

AC:

164

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

589

1178

1768

2357

2946

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

148

296

444

592

740

<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:

0.0841

Hom.:

207

Bravo

AF:

0.0767

Asia WGS

AF:

0.121

AC:

421

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

0.65

(source)

DANN

Benign

0.60

PhyloP100

-0.49

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