dbSNP rs1960350: LINC01499:n.37-5712C>T (chr11-41728960-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 ENST00000528720.5(LINC01499):n.37-5712C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.226 in 152,096 control chromosomes in the GnomAD database, including 4,162 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 0.23 ( 4162 hom., cov: 33)

Consequence

LINC01499
ENST00000528720.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.187

Publications

3 publications found

Variant links:

Genes affected

LINC01499 (HGNC:51165): (long intergenic non-protein coding RNA 1499)

LINC01499 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=-0.95).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.447 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LINC01499	NR_120584.1 link	n.37-5712C>T		intron_variant	Intron 1 of 5

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
LINC01499	ENST00000528720.5 link	n.37-5712C>T	intron_variant	Intron 1 of 5	4
LINC01499	ENST00000529282.1 link	n.169-5712C>T	intron_variant	Intron 2 of 5	4
LINC01499	ENST00000530379.1 link	n.473-5712C>T	intron_variant	Intron 1 of 1	4

Frequencies

GnomAD3 genomes

AF:

0.226

AC:

34372

AN:

151978

Hom.:

4159

Cov.:

show subpopulations

Gnomad AFR

AF:

0.216

Gnomad AMI

AF:

0.207

Gnomad AMR

AF:

0.285

Gnomad ASJ

AF:

0.239

Gnomad EAS

AF:

0.462

Gnomad SAS

AF:

0.229

Gnomad FIN

AF:

0.164

Gnomad MID

AF:

0.269

Gnomad NFE

AF:

0.209

Gnomad OTH

AF:

0.256

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

GnomAD4 genome

AF:

0.226

AC:

34411

AN:

152096

Hom.:

4162

Cov.:

AF XY:

0.226

AC XY:

16822

AN XY:

74360

show subpopulations

African (AFR)

AF:

0.216

AC:

8979

AN:

41512

American (AMR)

AF:

0.286

AC:

4364

AN:

15282

Ashkenazi Jewish (ASJ)

AF:

0.239

AC:

827

AN:

3466

East Asian (EAS)

AF:

0.462

AC:

2362

AN:

5112

South Asian (SAS)

AF:

0.228

AC:

1100

AN:

4830

European-Finnish (FIN)

AF:

0.164

AC:

1737

AN:

10598

Middle Eastern (MID)

AF:

0.269

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.209

AC:

14233

AN:

67976

Other (OTH)

AF:

0.256

AC:

542

AN:

2116

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.500

Heterozygous variant carriers

1384

2769

4153

5538

6922

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

360

720

1080

1440

1800

<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:

0.223

Hom.:

4830

Bravo

AF:

0.241

Asia WGS

AF:

0.343

AC:

1194

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

5.7

(source)

DANN

Benign

0.29

PhyloP100

0.19

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