NM_152311.5:c.410-1990A>G

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0820

Publications

10 publications found
Variant links:
Genes affected
CLRN3 (HGNC:20795): (clarin 3) Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]

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

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CLRN3NM_152311.5 linkc.410-1990A>G intron_variant Intron 2 of 2 ENST00000368671.4 NP_689524.1
CLRN3XM_011539274.3 linkc.230-1990A>G intron_variant Intron 1 of 1 XP_011537576.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CLRN3ENST00000368671.4 linkc.410-1990A>G intron_variant Intron 2 of 2 1 NM_152311.5 ENSP00000357660.3 Q8NCR9-1

Frequencies

GnomAD3 genomes
AF:
0.470
AC:
71423
AN:
151894
Hom.:
20246
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.145
Gnomad AMI
AF:
0.490
Gnomad AMR
AF:
0.556
Gnomad ASJ
AF:
0.504
Gnomad EAS
AF:
0.378
Gnomad SAS
AF:
0.543
Gnomad FIN
AF:
0.736
Gnomad MID
AF:
0.446
Gnomad NFE
AF:
0.607
Gnomad OTH
AF:
0.467
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.470
AC:
71425
AN:
152012
Hom.:
20251
Cov.:
31
AF XY:
0.478
AC XY:
35521
AN XY:
74288
show subpopulations
African (AFR)
AF:
0.145
AC:
6011
AN:
41494
American (AMR)
AF:
0.557
AC:
8495
AN:
15262
Ashkenazi Jewish (ASJ)
AF:
0.504
AC:
1750
AN:
3470
East Asian (EAS)
AF:
0.377
AC:
1934
AN:
5124
South Asian (SAS)
AF:
0.543
AC:
2616
AN:
4818
European-Finnish (FIN)
AF:
0.736
AC:
7795
AN:
10584
Middle Eastern (MID)
AF:
0.429
AC:
126
AN:
294
European-Non Finnish (NFE)
AF:
0.607
AC:
41263
AN:
67940
Other (OTH)
AF:
0.467
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:
0.559
Hom.:
40796
Bravo
AF:
0.440
Asia WGS
AF:
0.428
AC:
1487
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
CADD
Benign
2.5
DANN
Benign
0.63
PhyloP100
0.082
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.040
Details are displayed if max score is > 0.2

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

Publications

Other links and lift over

dbSNP: rs6482992; hg19: chr10-129678674; API