5-125011395-C-G

Variant summary

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

The ENST00000642715.2(LINC02240):​n.519+8382C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.249 in 152,112 control chromosomes in the GnomAD database, including 5,696 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 0.25 ( 5696 hom., cov: 32)

Consequence

LINC02240
ENST00000642715.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.240

Publications

8 publications found
Variant links:
Genes affected
LINC02240 (HGNC:53118): (long intergenic non-protein coding RNA 2240)

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=-0.81).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.422 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
LINC02240ENST00000642715.2 linkn.519+8382C>G intron_variant Intron 2 of 3
LINC02240ENST00000647105.1 linkn.205-30762C>G intron_variant Intron 1 of 6
LINC02240ENST00000671535.1 linkn.619+7634C>G intron_variant Intron 3 of 4
LINC02240ENST00000825653.1 linkn.349+8382C>G intron_variant Intron 2 of 2

Frequencies

GnomAD3 genomes
AF:
0.249
AC:
37821
AN:
151994
Hom.:
5680
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.426
Gnomad AMI
AF:
0.213
Gnomad AMR
AF:
0.187
Gnomad ASJ
AF:
0.136
Gnomad EAS
AF:
0.0218
Gnomad SAS
AF:
0.183
Gnomad FIN
AF:
0.219
Gnomad MID
AF:
0.228
Gnomad NFE
AF:
0.188
Gnomad OTH
AF:
0.244
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.249
AC:
37889
AN:
152112
Hom.:
5696
Cov.:
32
AF XY:
0.247
AC XY:
18337
AN XY:
74388
show subpopulations
African (AFR)
AF:
0.427
AC:
17707
AN:
41474
American (AMR)
AF:
0.187
AC:
2858
AN:
15276
Ashkenazi Jewish (ASJ)
AF:
0.136
AC:
473
AN:
3472
East Asian (EAS)
AF:
0.0218
AC:
113
AN:
5178
South Asian (SAS)
AF:
0.184
AC:
888
AN:
4826
European-Finnish (FIN)
AF:
0.219
AC:
2315
AN:
10590
Middle Eastern (MID)
AF:
0.235
AC:
69
AN:
294
European-Non Finnish (NFE)
AF:
0.188
AC:
12766
AN:
67982
Other (OTH)
AF:
0.240
AC:
506
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1364
2728
4091
5455
6819
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
366
732
1098
1464
1830
<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:
0.112
Hom.:
175
Bravo
AF:
0.255
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
-0.81
CADD
Benign
6.2
DANN
Benign
0.37
PhyloP100
0.24

Splicing

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

Publications

Other links and lift over

dbSNP: rs3936060; hg19: chr5-124347088; API