rs17192980
Variant names:
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
ENST00000512838.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.670
Publications
2 publications found
Genes affected
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 |
---|---|---|---|---|---|---|---|---|---|---|
LINC02196 | ENST00000512838.2 | n.69+43917T>C | intron_variant | Intron 1 of 6 | 4 | |||||
LINC02196 | ENST00000648809.1 | n.362+53727T>C | intron_variant | Intron 2 of 5 | ||||||
LINC02196 | ENST00000715905.1 | n.277+53727T>C | intron_variant | Intron 2 of 5 |
Frequencies
GnomAD3 genomes AF: 0.105 AC: 15949AN: 152144Hom.: 968 Cov.: 33 show subpopulations
GnomAD3 genomes
AF:
AC:
15949
AN:
152144
Hom.:
Cov.:
33
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.105 AC: 15970AN: 152262Hom.: 969 Cov.: 33 AF XY: 0.108 AC XY: 8022AN XY: 74458 show subpopulations
GnomAD4 genome
AF:
AC:
15970
AN:
152262
Hom.:
Cov.:
33
AF XY:
AC XY:
8022
AN XY:
74458
show subpopulations
African (AFR)
AF:
AC:
3234
AN:
41556
American (AMR)
AF:
AC:
2288
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
350
AN:
3472
East Asian (EAS)
AF:
AC:
505
AN:
5174
South Asian (SAS)
AF:
AC:
731
AN:
4826
European-Finnish (FIN)
AF:
AC:
1550
AN:
10600
Middle Eastern (MID)
AF:
AC:
53
AN:
294
European-Non Finnish (NFE)
AF:
AC:
6898
AN:
68022
Other (OTH)
AF:
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:
Hom.:
Bravo
AF:
Asia WGS
AF:
AC:
443
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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