NM_152311.5:c.410-1990A>G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_152311.5(CLRN3):c.410-1990A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.47 in 152,012 control chromosomes in the GnomAD database, including 20,251 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 0.47 ( 20251 hom., cov: 31)
Consequence
CLRN3
NM_152311.5 intron
NM_152311.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0820
Publications
10 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=-0.87).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.602 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.470 AC: 71423AN: 151894Hom.: 20246 Cov.: 31 show subpopulations
GnomAD3 genomes
AF:
AC:
71423
AN:
151894
Hom.:
Cov.:
31
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: 0.470 AC: 71425AN: 152012Hom.: 20251 Cov.: 31 AF XY: 0.478 AC XY: 35521AN XY: 74288 show subpopulations
GnomAD4 genome
AF:
AC:
71425
AN:
152012
Hom.:
Cov.:
31
AF XY:
AC XY:
35521
AN XY:
74288
show subpopulations
African (AFR)
AF:
AC:
6011
AN:
41494
American (AMR)
AF:
AC:
8495
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
AC:
1750
AN:
3470
East Asian (EAS)
AF:
AC:
1934
AN:
5124
South Asian (SAS)
AF:
AC:
2616
AN:
4818
European-Finnish (FIN)
AF:
AC:
7795
AN:
10584
Middle Eastern (MID)
AF:
AC:
126
AN:
294
European-Non Finnish (NFE)
AF:
AC:
41263
AN:
67940
Other (OTH)
AF:
AC:
989
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.503
Heterozygous variant carriers
0
1572
3143
4715
6286
7858
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
634
1268
1902
2536
3170
<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:
1487
AN:
3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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