NM_006235.3:c.16+5131T>C
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_006235.3(POU2AF1):c.16+5131T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.648 in 151,736 control chromosomes in the GnomAD database, including 33,267 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 0.65 ( 33267 hom., cov: 30)
Consequence
POU2AF1
NM_006235.3 intron
NM_006235.3 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.0120
Publications
3 publications found
Genes affected
POU2AF1 (HGNC:9211): (POU class 2 homeobox associating factor 1) Enables transcription coactivator activity. Involved in positive regulation of transcription by RNA polymerase II. Part of RNA polymerase II transcription regulator complex. [provided by Alliance of Genome Resources, Apr 2022]
POU2AF1 Gene-Disease associations (from GenCC):
- agammaglobulinemiaInheritance: AR Classification: LIMITED Submitted by: ClinGen
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=-0.74).
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.762 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
POU2AF1 | ENST00000393067.8 | c.16+5131T>C | intron_variant | Intron 1 of 4 | 1 | NM_006235.3 | ENSP00000376786.3 | |||
POU2AF1 | ENST00000531398.1 | c.23-15113T>C | intron_variant | Intron 2 of 4 | 4 | ENSP00000433527.1 | ||||
POU2AF1 | ENST00000526535.1 | n.114+5131T>C | intron_variant | Intron 1 of 1 | 4 | |||||
POU2AF1 | ENST00000530793.5 | n.193+3743T>C | intron_variant | Intron 2 of 2 | 3 |
Frequencies
GnomAD3 genomes AF: 0.648 AC: 98255AN: 151616Hom.: 33267 Cov.: 30 show subpopulations
GnomAD3 genomes
AF:
AC:
98255
AN:
151616
Hom.:
Cov.:
30
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: 0.648 AC: 98287AN: 151736Hom.: 33267 Cov.: 30 AF XY: 0.642 AC XY: 47609AN XY: 74138 show subpopulations
GnomAD4 genome
AF:
AC:
98287
AN:
151736
Hom.:
Cov.:
30
AF XY:
AC XY:
47609
AN XY:
74138
show subpopulations
African (AFR)
AF:
AC:
19747
AN:
41308
American (AMR)
AF:
AC:
11795
AN:
15248
Ashkenazi Jewish (ASJ)
AF:
AC:
2537
AN:
3468
East Asian (EAS)
AF:
AC:
2091
AN:
5170
South Asian (SAS)
AF:
AC:
2104
AN:
4822
European-Finnish (FIN)
AF:
AC:
6944
AN:
10430
Middle Eastern (MID)
AF:
AC:
208
AN:
294
European-Non Finnish (NFE)
AF:
AC:
50691
AN:
67978
Other (OTH)
AF:
AC:
1445
AN:
2108
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.499
Heterozygous variant carriers
0
1592
3184
4776
6368
7960
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
780
1560
2340
3120
3900
<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:
1412
AN:
3476
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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