dbSNP rs71057061: POU2AF1:c.147+90_147+91dupAG (chr11-111358696-A-ACT) – ACMG Classification: Benign (-10 pts)

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

Publications

1 publications found

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]

POU2AF1 Gene-Disease associations (from GenCC):

agammaglobulinemia
Inheritance: AR Classification: LIMITED Submitted by: ClinGen

POU2AF1 links:

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 VariationId 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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006235.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2AF1	NM_006235.3	MANE Select	c.147+90_147+91dupAG		intron	N/A	NP_006226.2	Q16633

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
POU2AF1	ENST00000393067.8	TSL:1 MANE Select	c.147+91_147+92insAG	intron	N/A	ENSP00000376786.3	Q16633
POU2AF1	ENST00000531398.1	TSL:4	c.153+91_153+92insAG	intron	N/A	ENSP00000433527.1	E9PKH4
POU2AF1	ENST00000525584.1	TSL:3	n.266+91_266+92insAG	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.681

AC:

101587

AN:

149180

Hom.:

35104

Cov.:

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

African (AFR)

AF:

0.584

AC:

16739

AN:

28654

American (AMR)

AF:

0.813

AC:

28759

AN:

35370

Ashkenazi Jewish (ASJ)

AF:

0.755

AC:

18213

AN:

24112

East Asian (EAS)

AF:

0.412

AC:

14298

AN:

34678

South Asian (SAS)

AF:

0.475

AC:

35681

AN:

75138

European-Finnish (FIN)

AF:

0.677

AC:

23474

AN:

34688

Middle Eastern (MID)

AF:

0.682

AC:

2891

AN:

4242

European-Non Finnish (NFE)

AF:

0.741

AC:

710267

AN:

958178

Other (OTH)

AF:

0.695

AC:

37110

AN:

53382

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.499

Heterozygous variant carriers

12054

24108

36163

48217

60271

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

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.:

AF XY:

0.675

AC XY:

49172

AN XY:

72848

show subpopulations

African (AFR)

AF:

0.601

AC:

24344

AN:

40492

American (AMR)

AF:

0.782

AC:

11795

AN:

15084

Ashkenazi Jewish (ASJ)

AF:

0.752

AC:

2571

AN:

3418

East Asian (EAS)

AF:

0.405

AC:

1999

AN:

4932

South Asian (SAS)

AF:

0.468

AC:

2210

AN:

4726

European-Finnish (FIN)

AF:

0.659

AC:

6744

AN:

10228

Middle Eastern (MID)

AF:

0.716

AC:

202

AN:

282

European-Non Finnish (NFE)

AF:

0.738

AC:

49593

AN:

67162

Other (OTH)

AF:

0.711

AC:

1477

AN:

2078

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.487

Heterozygous variant carriers

1454

2908

4362

5816

7270

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

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

ClinVar submissions

Significance:Benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not specified (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.6

Mutation Taster

=100/0

polymorphism (auto)

(source)

Splicing

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over