rs1944932

chr11-111431285-T-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000515029.2(POU2AF1):n.53+3707A>T variant causes a intron, non coding transcript 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 ENST00000515029.2 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.05

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:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BTG4	XM_011542876.3	c.663-26563A>T		intron_variant
BTG4	XM_024448587.2	c.663-26563A>T		intron_variant
BTG4	XM_024448588.2	c.663-26563A>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU2AF1	ENST00000515029.2	n.53+3707A>T		intron_variant, non_coding_transcript_variant		1
POU2AF1	ENST00000531398.1	c.-81+18634A>T		intron_variant		4
POU2AF1	ENST00000525890.1	n.412+23934A>T		intron_variant, non_coding_transcript_variant		3

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

Gnomad4 AFR AF: 0.684

Gnomad4 AMR AF: 0.472

Gnomad4 ASJ AF: 0.460

Gnomad4 EAS AF: 0.292

Gnomad4 SAS AF: 0.352

Gnomad4 FIN AF: 0.456

Gnomad4 NFE AF: 0.429

Gnomad4 OTH AF: 0.472

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 v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	4.9
Dann	Benign	0.50

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1944932; hg19: chr11-111302010;