rs11213809

Positions:

• chr11-111265020-A-G
• chr11-111265020-A-T

Variant summary

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

The NM_198498.3(POU2AF2):​c.120+8928A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.742 in 151,702 control chromosomes in the GnomAD database, including 42,158 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 0.74 (42158 hom., cov: 28)
• Consequence: POU2AF2 NM_198498.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.771

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.01).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
POU2AF2	NM_198498.3	c.120+8928A>G		intron_variant		ENST00000280325.7	NP_940900.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
POU2AF2	ENST00000280325.7	c.120+8928A>G		intron_variant		5	NM_198498.3	ENSP00000280325.6
POU2AF2	ENST00000637637.1	c.-37+8928A>G		intron_variant		1		ENSP00000489630.1
POU2AF2	ENST00000635886.1	n.120+8928A>G		intron_variant		5		ENSP00000489980.1
POU2AF2	ENST00000667535.1	n.110+8928A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.742 AC: 112518 AN: 151584 Hom.: 42103 Cov.: 28

Gnomad AFR AF: 0.800

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.791

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.829

Gnomad FIN AF: 0.778

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.683

Gnomad OTH AF: 0.728

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

GnomAD4 genome AF: 0.742 AC: 112630 AN: 151702 Hom.: 42158 Cov.: 28 AF XY: 0.749 AC XY: 55549 AN XY: 74122

Gnomad4 AFR AF: 0.800

Gnomad4 AMR AF: 0.791

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.828

Gnomad4 FIN AF: 0.778

Gnomad4 NFE AF: 0.683

Gnomad4 OTH AF: 0.730

Alfa AF: 0.697 Hom.: 75138

Bravo AF: 0.742

Asia WGS AF: 0.846 AC: 2938 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.37
DANN	Benign	0.42

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: rs11213809; hg19: chr11-111135745;