11-111358696-A-ACT

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_006235.3(POU2AF1):​c.147+90_147+91dupAG variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.708 in 1,397,740 control chromosomes in the GnomAD database, including 359,529 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.68 ( 35119 hom., cov: 0)
Exomes 𝑓: 0.71 ( 324410 hom. )

Consequence

POU2AF1
NM_006235.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 1.64
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -10 ACMG points.

BP6
Variant 11-111358696-A-ACT is Benign according to our data. Variant chr11-111358696-A-ACT is described in ClinVar as [Benign]. Clinvar id is 2688270.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.77 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
POU2AF1NM_006235.3 linkc.147+90_147+91dupAG intron_variant Intron 2 of 4 ENST00000393067.8 NP_006226.2 Q16633

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
POU2AF1ENST00000393067.8 linkc.147+91_147+92insAG intron_variant Intron 2 of 4 1 NM_006235.3 ENSP00000376786.3 Q16633

Frequencies

GnomAD3 genomes
AF:
0.681
AC:
101587
AN:
149180
Hom.:
35104
Cov.:
0
show subpopulations
Gnomad AFR
AF:
0.601
Gnomad AMI
AF:
0.797
Gnomad AMR
AF:
0.782
Gnomad ASJ
AF:
0.752
Gnomad EAS
AF:
0.406
Gnomad SAS
AF:
0.467
Gnomad FIN
AF:
0.659
Gnomad MID
AF:
0.720
Gnomad NFE
AF:
0.738
Gnomad OTH
AF:
0.713
GnomAD4 exome
AF:
0.711
AC:
887432
AN:
1248442
Hom.:
324410
AF XY:
0.703
AC XY:
437159
AN XY:
621822
show subpopulations
Gnomad4 AFR exome
AF:
0.584
AC:
16739
AN:
28654
Gnomad4 AMR exome
AF:
0.813
AC:
28759
AN:
35370
Gnomad4 ASJ exome
AF:
0.755
AC:
18213
AN:
24112
Gnomad4 EAS exome
AF:
0.412
AC:
14298
AN:
34678
Gnomad4 SAS exome
AF:
0.475
AC:
35681
AN:
75138
Gnomad4 FIN exome
AF:
0.677
AC:
23474
AN:
34688
Gnomad4 NFE exome
AF:
0.741
AC:
710267
AN:
958178
Gnomad4 Remaining exome
AF:
0.695
AC:
37110
AN:
53382
Heterozygous variant carriers
0
12054
24108
36163
48217
60271
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Exome Het
Exome Hom
Variant carriers
0
16546
33092
49638
66184
82730
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
GnomAD4 genome
AF:
0.681
AC:
101649
AN:
149298
Hom.:
35119
Cov.:
0
AF XY:
0.675
AC XY:
49172
AN XY:
72848
show subpopulations
Gnomad4 AFR
AF:
0.601
AC:
0.601205
AN:
0.601205
Gnomad4 AMR
AF:
0.782
AC:
0.781954
AN:
0.781954
Gnomad4 ASJ
AF:
0.752
AC:
0.752194
AN:
0.752194
Gnomad4 EAS
AF:
0.405
AC:
0.405312
AN:
0.405312
Gnomad4 SAS
AF:
0.468
AC:
0.467626
AN:
0.467626
Gnomad4 FIN
AF:
0.659
AC:
0.659366
AN:
0.659366
Gnomad4 NFE
AF:
0.738
AC:
0.738409
AN:
0.738409
Gnomad4 OTH
AF:
0.711
AC:
0.71078
AN:
0.71078
Heterozygous variant carriers
0
1454
2908
4362
5816
7270
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Genome Het
Genome Hom
Variant carriers
0
792
1584
2376
3168
3960
<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:
0.544
Hom.:
1146

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Benign:1
Jan 24, 2024
Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan
Significance:Benign
Review Status:criteria provided, single submitter
Collection Method:clinical testing

This variant is classified as Benign based on local population frequency. This variant was detected in 27% of patients studied by a panel of primary immunodeficiencies. Number of patients: 26. Only high quality variants are reported. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
Mutation Taster
=100/0
polymorphism (auto)

Splicing

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs71057061; hg19: chr11-111229421; API