chr15-53203733-T-C

Variant summary

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

The ENST00000780988.1(LINC02490):​n.310-5126T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.323 in 151,972 control chromosomes in the GnomAD database, including 8,130 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 0.32 ( 8130 hom., cov: 32)

Consequence

LINC02490
ENST00000780988.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.602

Publications

4 publications found
Variant links:
Genes affected
LINC02490 (HGNC:53471): (long intergenic non-protein coding RNA 2490)

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 (EAS) allele frequency at 95% confidence interval = 0.484 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
LOC107983981XR_004837531.2 linkn.481-17693T>C intron_variant Intron 4 of 4
LOC107983981XR_932257.3 linkn.696+9890T>C intron_variant Intron 5 of 5

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02490ENST00000780988.1 linkn.310-5126T>C intron_variant Intron 2 of 3

Frequencies

GnomAD3 genomes
AF:
0.323
AC:
49025
AN:
151854
Hom.:
8118
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.300
Gnomad AMI
AF:
0.178
Gnomad AMR
AF:
0.389
Gnomad ASJ
AF:
0.317
Gnomad EAS
AF:
0.500
Gnomad SAS
AF:
0.381
Gnomad FIN
AF:
0.392
Gnomad MID
AF:
0.323
Gnomad NFE
AF:
0.296
Gnomad OTH
AF:
0.309
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.323
AC:
49072
AN:
151972
Hom.:
8130
Cov.:
32
AF XY:
0.332
AC XY:
24643
AN XY:
74292
show subpopulations
African (AFR)
AF:
0.300
AC:
12457
AN:
41468
American (AMR)
AF:
0.389
AC:
5939
AN:
15264
Ashkenazi Jewish (ASJ)
AF:
0.317
AC:
1101
AN:
3470
East Asian (EAS)
AF:
0.500
AC:
2561
AN:
5120
South Asian (SAS)
AF:
0.380
AC:
1829
AN:
4808
European-Finnish (FIN)
AF:
0.392
AC:
4144
AN:
10574
Middle Eastern (MID)
AF:
0.316
AC:
93
AN:
294
European-Non Finnish (NFE)
AF:
0.296
AC:
20122
AN:
67954
Other (OTH)
AF:
0.315
AC:
664
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.502
Heterozygous variant carriers
0
1675
3349
5024
6698
8373
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
486
972
1458
1944
2430
<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:
0.301
Hom.:
21069
Bravo
AF:
0.324
Asia WGS
AF:
0.434
AC:
1507
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
1.3
DANN
Benign
0.48
PhyloP100
-0.60

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

Other links and lift over

dbSNP: rs518127; hg19: chr15-53495930; API