11-111358696-A-ACT

Variant names:

• chr11-111358696-A-ACT
• rs71057061
• NM_006235.3:c.147+90_147+91dupAG

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

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
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.64

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]

ACMG classification

Verdict is Benign. Variant got -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
POU2AF1	NM_006235.3	c.147+90_147+91dupAG		intron_variant	Intron 2 of 4	ENST00000393067.8	NP_006226.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POU2AF1	ENST00000393067.8	c.147+91_147+92insAG		intron_variant	Intron 2 of 4	1	NM_006235.3	ENSP00000376786.3
POU2AF1	ENST00000531398.1	c.153+91_153+92insAG		intron_variant	Intron 3 of 4	4		ENSP00000433527.1
POU2AF1	ENST00000525584.1	n.266+91_266+92insAG		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.681 AC: 101587 AN: 149180 Hom.: 35104 Cov.: 0

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

Gnomad4 AFR exome AF: 0.584

Gnomad4 AMR exome AF: 0.813

Gnomad4 ASJ exome AF: 0.755

Gnomad4 EAS exome AF: 0.412

Gnomad4 SAS exome AF: 0.475

Gnomad4 FIN exome AF: 0.677

Gnomad4 NFE exome AF: 0.741

Gnomad4 OTH exome AF: 0.695

GnomAD4 genome AF: 0.681 AC: 101649 AN: 149298 Hom.: 35119 Cov.: 0 AF XY: 0.675 AC XY: 49172 AN XY: 72848

Gnomad4 AFR AF: 0.601

Gnomad4 AMR AF: 0.782

Gnomad4 ASJ AF: 0.752

Gnomad4 EAS AF: 0.405

Gnomad4 SAS AF: 0.468

Gnomad4 FIN AF: 0.659

Gnomad4 NFE AF: 0.738

Gnomad4 OTH AF: 0.711

Alfa AF: 0.544 Hom.: 1146

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs71057061; hg19: chr11-111229421;