2-165514316-A-C

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.40

Publications

6 publications found
Variant links:
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]

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=-0.92).
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
CSRNP3NM_001172173.2 linkc.-112-3557A>C intron_variant Intron 2 of 6 ENST00000651982.1 NP_001165644.1 Q8WYN3-1
CSRNP3XM_024453155.2 linkc.-112-3557A>C intron_variant Intron 3 of 7 XP_024308923.1
CSRNP3XM_047445908.1 linkc.-112-3557A>C intron_variant Intron 2 of 6 XP_047301864.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CSRNP3ENST00000651982.1 linkc.-112-3557A>C intron_variant Intron 2 of 6 NM_001172173.2 ENSP00000498841.1 Q8WYN3-1

Frequencies

GnomAD3 genomes
AF:
0.731
AC:
111175
AN:
152084
Hom.:
41387
Cov.:
34
show subpopulations
Gnomad AFR
AF:
0.869
Gnomad AMI
AF:
0.627
Gnomad AMR
AF:
0.731
Gnomad ASJ
AF:
0.643
Gnomad EAS
AF:
0.796
Gnomad SAS
AF:
0.617
Gnomad FIN
AF:
0.698
Gnomad MID
AF:
0.522
Gnomad NFE
AF:
0.663
Gnomad OTH
AF:
0.705
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.731
AC:
111301
AN:
152202
Hom.:
41454
Cov.:
34
AF XY:
0.731
AC XY:
54367
AN XY:
74398
show subpopulations
African (AFR)
AF:
0.870
AC:
36121
AN:
41532
American (AMR)
AF:
0.732
AC:
11195
AN:
15292
Ashkenazi Jewish (ASJ)
AF:
0.643
AC:
2229
AN:
3466
East Asian (EAS)
AF:
0.796
AC:
4111
AN:
5164
South Asian (SAS)
AF:
0.616
AC:
2972
AN:
4824
European-Finnish (FIN)
AF:
0.698
AC:
7393
AN:
10594
Middle Eastern (MID)
AF:
0.514
AC:
151
AN:
294
European-Non Finnish (NFE)
AF:
0.663
AC:
45060
AN:
68008
Other (OTH)
AF:
0.707
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:
0.700
Hom.:
19988
Bravo
AF:
0.742
Asia WGS
AF:
0.726
AC:
2521
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.92
CADD
Benign
0.66
DANN
Benign
0.66
PhyloP100
-1.4
Mutation Taster
=100/0
polymorphism (auto)

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
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: rs6432832; hg19: chr2-166370826; API