11-111286111-T-C

Variant names:

• chr11-111286111-T-C
• rs3087967
• NM_198498.3:c.*57T>C

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 38 publications found

Genes affected

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

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

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198498.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2AF2	NM_198498.3	MANE Select	c.*57T>C		3_prime_UTR	Exon 5 of 5	NP_940900.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2AF2	ENST00000280325.7	TSL:5 MANE Select	c.*57T>C		3_prime_UTR	Exon 5 of 5	ENSP00000280325.6
	POU2AF2	ENST00000637637.1	TSL:1	c.*57T>C		3_prime_UTR	Exon 4 of 4	ENSP00000489630.1
	POU2AF2	ENST00000667535.1		n.914T>C		non_coding_transcript_exon	Exon 4 of 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

African (AFR) AF: 0.708 AC: 22130 AN: 31260

American (AMR) AF: 0.809 AC: 27602 AN: 34100

Ashkenazi Jewish (ASJ) AF: 0.717 AC: 17693 AN: 24692

East Asian (EAS) AF: 0.622 AC: 24124 AN: 38804

South Asian (SAS) AF: 0.830 AC: 66200 AN: 79714

European-Finnish (FIN) AF: 0.772 AC: 40729 AN: 52768

Middle Eastern (MID) AF: 0.791 AC: 4435 AN: 5606

European-Non Finnish (NFE) AF: 0.705 AC: 773743 AN: 1098208

Other (OTH) AF: 0.714 AC: 41996 AN: 58820

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

African (AFR) AF: 0.707 AC: 29323 AN: 41488

American (AMR) AF: 0.785 AC: 12002 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.727 AC: 2521 AN: 3470

East Asian (EAS) AF: 0.592 AC: 3045 AN: 5146

South Asian (SAS) AF: 0.826 AC: 3990 AN: 4828

European-Finnish (FIN) AF: 0.775 AC: 8197 AN: 10582

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.717 AC: 48726 AN: 67974

Other (OTH) AF: 0.730 AC: 1540 AN: 2110

Alfa AF: 0.721 Hom.: 64866

Bravo AF: 0.719

Asia WGS AF: 0.762 AC: 2648 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	0.025
DANN	Benign	0.23
PhyloP100		-3.5
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3087967; hg19: chr11-111156836; COSMIC: COSV107244791; COSMIC: COSV107244791;