rs11213809

Variant names:

• chr11-111265020-A-G
• rs11213809
• NM_198498.3:c.120+8928A>G

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 6 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=-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 rank	MANE	Protein	UniProt
POU2AF2	NM_198498.3	c.120+8928A>G		intron_variant	Intron 2 of 4	ENST00000280325.7	NP_940900.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POU2AF2	ENST00000280325.7	c.120+8928A>G		intron_variant	Intron 2 of 4	5	NM_198498.3	ENSP00000280325.6
POU2AF2	ENST00000637637.1	c.-37+8928A>G		intron_variant	Intron 1 of 3	1		ENSP00000489630.1
POU2AF2	ENST00000635886.1	n.120+8928A>G		intron_variant	Intron 2 of 3	5		ENSP00000489980.1
POU2AF2	ENST00000667535.1	n.110+8928A>G		intron_variant	Intron 1 of 3

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

African (AFR) AF: 0.800 AC: 33072 AN: 41346

American (AMR) AF: 0.791 AC: 12062 AN: 15256

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2403 AN: 3466

East Asian (EAS) AF: 0.841 AC: 4304 AN: 5116

South Asian (SAS) AF: 0.828 AC: 3965 AN: 4788

European-Finnish (FIN) AF: 0.778 AC: 8172 AN: 10508

Middle Eastern (MID) AF: 0.813 AC: 239 AN: 294

European-Non Finnish (NFE) AF: 0.683 AC: 46411 AN: 67912

Other (OTH) AF: 0.730 AC: 1538 AN: 2106

Alfa AF: 0.703 Hom.: 114972

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
PhyloP100		-0.77
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: rs11213809; hg19: chr11-111135745;