2-165514316-A-C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001172173.2(CSRNP3):c.-112-3557A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.731 in 152,202 control chromosomes in the GnomAD database, including 41,454 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 0.73 ( 41454 hom., cov: 34)
Consequence
CSRNP3
NM_001172173.2 intron
NM_001172173.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.40
Publications
6 publications found
Genes affected
CSRNP3 (HGNC:30729): (cysteine and serine rich nuclear protein 3) Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and sequence-specific DNA binding activity. Predicted to be involved in positive regulation of apoptotic process and positive regulation of transcription by RNA polymerase II. Predicted to be part of chromatin. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.92).
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.862 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CSRNP3 | NM_001172173.2 | c.-112-3557A>C | intron_variant | Intron 2 of 6 | ENST00000651982.1 | NP_001165644.1 | ||
CSRNP3 | XM_024453155.2 | c.-112-3557A>C | intron_variant | Intron 3 of 7 | XP_024308923.1 | |||
CSRNP3 | XM_047445908.1 | c.-112-3557A>C | intron_variant | Intron 2 of 6 | XP_047301864.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.731 AC: 111175AN: 152084Hom.: 41387 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
111175
AN:
152084
Hom.:
Cov.:
34
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: 0.731 AC: 111301AN: 152202Hom.: 41454 Cov.: 34 AF XY: 0.731 AC XY: 54367AN XY: 74398 show subpopulations
GnomAD4 genome
AF:
AC:
111301
AN:
152202
Hom.:
Cov.:
34
AF XY:
AC XY:
54367
AN XY:
74398
show subpopulations
African (AFR)
AF:
AC:
36121
AN:
41532
American (AMR)
AF:
AC:
11195
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
AC:
2229
AN:
3466
East Asian (EAS)
AF:
AC:
4111
AN:
5164
South Asian (SAS)
AF:
AC:
2972
AN:
4824
European-Finnish (FIN)
AF:
AC:
7393
AN:
10594
Middle Eastern (MID)
AF:
AC:
151
AN:
294
European-Non Finnish (NFE)
AF:
AC:
45060
AN:
68008
Other (OTH)
AF:
AC:
1497
AN:
2116
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.501
Heterozygous variant carriers
0
1492
2984
4475
5967
7459
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
830
1660
2490
3320
4150
<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:
2521
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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