11-111286111-T-C

Position:

• chr11-111286111-T-C

Variant summary

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

The NM_198498.3(POU2AF2):​c.*57T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.716 in 1,576,064 control chromosomes in the GnomAD database, including 405,768 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 0.72 (39954 hom., cov: 31)
  • Exomes 𝑓: 0.72 (365814 hom.)
• Consequence: POU2AF2 NM_198498.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.47

Genes affected

POU2AF2 (HGNC:30527): (POU class 2 homeobox associating factor 2)

POU2AF2 (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 (SAS) allele frequency at 95% confidence interval = 0.805 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POU2AF2	NM_198498.3	c.*57T>C		3_prime_UTR_variant	5/5	ENST00000280325.7	NP_940900.2
POU2AF2	XM_011542804.3	c.*57T>C		3_prime_UTR_variant	4/4		XP_011541106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POU2AF2	ENST00000280325.7	c.*57T>C		3_prime_UTR_variant	5/5	5	NM_198498.3	ENSP00000280325.6
POU2AF2	ENST00000637637.1	c.*57T>C		3_prime_UTR_variant	4/4	1		ENSP00000489630.1
POU2AF2	ENST00000667535.1	n.914T>C		non_coding_transcript_exon_variant	4/4

Frequencies

GnomAD3 genomes AF: 0.724 AC: 109992 AN: 151974 Hom.: 39917 Cov.: 31

Gnomad AFR AF: 0.707

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.785

Gnomad ASJ AF: 0.727

Gnomad EAS AF: 0.592

Gnomad SAS AF: 0.826

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.820

Gnomad NFE AF: 0.717

Gnomad OTH AF: 0.726

GnomAD4 exome AF: 0.715 AC: 1018652 AN: 1423972 Hom.: 365814 Cov.: 30 AF XY: 0.719 AC XY: 509100 AN XY: 707694

Gnomad4 AFR exome AF: 0.708

Gnomad4 AMR exome AF: 0.809

Gnomad4 ASJ exome AF: 0.717

Gnomad4 EAS exome AF: 0.622

Gnomad4 SAS exome AF: 0.830

Gnomad4 FIN exome AF: 0.772

Gnomad4 NFE exome AF: 0.705

Gnomad4 OTH exome AF: 0.714

GnomAD4 genome AF: 0.724 AC: 110086 AN: 152092 Hom.: 39954 Cov.: 31 AF XY: 0.728 AC XY: 54129 AN XY: 74368

Gnomad4 AFR AF: 0.707

Gnomad4 AMR AF: 0.785

Gnomad4 ASJ AF: 0.727

Gnomad4 EAS AF: 0.592

Gnomad4 SAS AF: 0.826

Gnomad4 FIN AF: 0.775

Gnomad4 NFE AF: 0.717

Gnomad4 OTH AF: 0.730

Alfa AF: 0.720 Hom.: 45119

Bravo AF: 0.719

Asia WGS AF: 0.762 AC: 2648 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	0.025
DANN	Benign	0.23

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs3087967; hg19: chr11-111156836;