11-111430057-T-G

Position:

• chr11-111430057-T-G

Variant summary

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

The ENST00000531398.1(POU2AF1):​c.-81+19862A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.347 in 152,088 control chromosomes in the GnomAD database, including 9,226 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 0.35 (9226 hom., cov: 33)
• Consequence: POU2AF1 ENST00000531398.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0550

Genes affected

POU2AF1 (HGNC:):

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.386 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
BTG4	XM_024448587.2	c.663-25335A>C		intron_variant			XP_024304355.1
BTG4	XM_024448588.2	c.663-25335A>C		intron_variant			XP_024304356.1
BTG4	XM_024448589.2	c.663-25335A>C		intron_variant			XP_024304357.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POU2AF1	ENST00000515029.2	n.53+4935A>C		intron_variant		1
POU2AF1	ENST00000531398.1	c.-81+19862A>C		intron_variant		4		ENSP00000433527.1
POU2AF1	ENST00000525890.1	n.412+25162A>C		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.347 AC: 52706 AN: 151970 Hom.: 9201 Cov.: 33

Gnomad AFR AF: 0.391

Gnomad AMI AF: 0.159

Gnomad AMR AF: 0.362

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.288

Gnomad SAS AF: 0.325

Gnomad FIN AF: 0.396

Gnomad MID AF: 0.377

Gnomad NFE AF: 0.317

Gnomad OTH AF: 0.335

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

GnomAD4 genome AF: 0.347 AC: 52777 AN: 152088 Hom.: 9226 Cov.: 33 AF XY: 0.350 AC XY: 25996 AN XY: 74346

Gnomad4 AFR AF: 0.391

Gnomad4 AMR AF: 0.362

Gnomad4 ASJ AF: 0.359

Gnomad4 EAS AF: 0.288

Gnomad4 SAS AF: 0.326

Gnomad4 FIN AF: 0.396

Gnomad4 NFE AF: 0.317

Gnomad4 OTH AF: 0.338

Alfa AF: 0.337 Hom.: 1444

Bravo AF: 0.349

Asia WGS AF: 0.298 AC: 1037 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	1.9
DANN	Benign	0.38

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs4936453; hg19: chr11-111300782;