11-111358696-A-ACT

Position:

• chr11-111358696-A-ACT

Variant summary

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

The NM_006235.3(POU2AF1):​c.147+91_147+92insAG 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/exons	MANE	UniProt
POU2AF1	NM_006235.3	c.147+91_147+92insAG		intron_variant		ENST00000393067.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU2AF1	ENST00000393067.8	c.147+91_147+92insAG		intron_variant		1	NM_006235.3	P1
POU2AF1	ENST00000531398.1	c.153+91_153+92insAG		intron_variant		4
POU2AF1	ENST00000525584.1	n.266+91_266+92insAG		intron_variant, non_coding_transcript_variant		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

Benign, criteria provided, single submitter

clinical testing

Unidad de Genómica Garrahan, Hospital de Pediatría Garrahan

Jan 24, 2024

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;