rs1944932

Variant names:

• chr11-111431285-T-A
• rs1944932
• ENST00000515029.2:n.53+3707A>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000531398.1(POU2AF1):​c.-81+18634A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.498 in 151,938 control chromosomes in the GnomAD database, including 20,035 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 0.50 (20035 hom., cov: 31)
• Consequence: POU2AF1 ENST00000531398.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05
• Publications: 2 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]

BTG4 (HGNC:13862): (BTG anti-proliferation factor 4) The protein encoded by this gene is a member of the BTG/Tob family. This family has structurally related proteins that appear to have antiproliferative properties. This encoded protein can induce G1 arrest in the cell cycle. [provided by RefSeq, Jul 2008]

BTG4 Gene-Disease associations (from GenCC):

• oocyte maturation defect 8

  Inheritance: AR Classification: STRONG, LIMITED Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
• female infertility

  Inheritance: AR Classification: MODERATE Submitted by: Franklin by Genoox

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.677 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000531398.1. 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
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2AF1	ENST00000515029.2	TSL:1	n.53+3707A>T		intron	N/A
	POU2AF1	ENST00000531398.1	TSL:4	c.-81+18634A>T		intron	N/A	ENSP00000433527.1	E9PKH4
	POU2AF1	ENST00000525890.1	TSL:3	n.412+23934A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.498 AC: 75586 AN: 151820 Hom.: 19976 Cov.: 31

Gnomad AFR AF: 0.683

Gnomad AMI AF: 0.287

Gnomad AMR AF: 0.472

Gnomad ASJ AF: 0.460

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.352

Gnomad FIN AF: 0.456

Gnomad MID AF: 0.513

Gnomad NFE AF: 0.429

Gnomad OTH AF: 0.470

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.498 AC: 75707 AN: 151938 Hom.: 20035 Cov.: 31 AF XY: 0.495 AC XY: 36755 AN XY: 74268

African (AFR) AF: 0.684 AC: 28341 AN: 41456

American (AMR) AF: 0.472 AC: 7197 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.460 AC: 1595 AN: 3466

East Asian (EAS) AF: 0.292 AC: 1512 AN: 5172

South Asian (SAS) AF: 0.352 AC: 1693 AN: 4804

European-Finnish (FIN) AF: 0.456 AC: 4807 AN: 10544

Middle Eastern (MID) AF: 0.517 AC: 152 AN: 294

European-Non Finnish (NFE) AF: 0.429 AC: 29155 AN: 67934

Other (OTH) AF: 0.472 AC: 993 AN: 2106

Alfa AF: 0.478 Hom.: 2224

Bravo AF: 0.510

Asia WGS AF: 0.344 AC: 1201 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	4.9
DANN	Benign	0.50
PhyloP100		1.0

Splicing

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

Other links and lift over

dbSNP: rs1944932; hg19: chr11-111302010;