rs17192980

Variant summary

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

The ENST00000512838.2(LINC02196):​n.69+43917T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.105 in 152,262 control chromosomes in the GnomAD database, including 969 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 0.10 ( 969 hom., cov: 33)

Consequence

LINC02196
ENST00000512838.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.670

Publications

2 publications found
Variant links:
Genes affected
LINC02196 (HGNC:53062): (long intergenic non-protein coding RNA 2196)

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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.145 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
LINC02196ENST00000512838.2 linkn.69+43917T>C intron_variant Intron 1 of 6 4
LINC02196ENST00000648809.1 linkn.362+53727T>C intron_variant Intron 2 of 5
LINC02196ENST00000715905.1 linkn.277+53727T>C intron_variant Intron 2 of 5

Frequencies

GnomAD3 genomes
AF:
0.105
AC:
15949
AN:
152144
Hom.:
968
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.0774
Gnomad AMI
AF:
0.143
Gnomad AMR
AF:
0.150
Gnomad ASJ
AF:
0.101
Gnomad EAS
AF:
0.0976
Gnomad SAS
AF:
0.151
Gnomad FIN
AF:
0.146
Gnomad MID
AF:
0.187
Gnomad NFE
AF:
0.101
Gnomad OTH
AF:
0.110
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.105
AC:
15970
AN:
152262
Hom.:
969
Cov.:
33
AF XY:
0.108
AC XY:
8022
AN XY:
74458
show subpopulations
African (AFR)
AF:
0.0778
AC:
3234
AN:
41556
American (AMR)
AF:
0.150
AC:
2288
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.101
AC:
350
AN:
3472
East Asian (EAS)
AF:
0.0976
AC:
505
AN:
5174
South Asian (SAS)
AF:
0.151
AC:
731
AN:
4826
European-Finnish (FIN)
AF:
0.146
AC:
1550
AN:
10600
Middle Eastern (MID)
AF:
0.180
AC:
53
AN:
294
European-Non Finnish (NFE)
AF:
0.101
AC:
6898
AN:
68022
Other (OTH)
AF:
0.109
AC:
231
AN:
2114
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
724
1448
2172
2896
3620
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance

Age Distribution

Genome Het
Genome Hom
Variant carriers
0
184
368
552
736
920
<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:
0.105
Hom.:
1474
Bravo
AF:
0.106
Asia WGS
AF:
0.128
AC:
443
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.90
CADD
Benign
6.6
DANN
Benign
0.72
PhyloP100
-0.67

Splicing

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

Publications

Other links and lift over

dbSNP: rs17192980; hg19: chr5-6977768; API