11-111283347-A-T

Variant names:

• chr11-111283347-A-T
• rs7130173
• NM_198498.3:c.164-729A>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The NM_198498.3(POU2AF2):​c.164-729A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 30)
• Consequence: POU2AF2 NM_198498.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.786
• Publications: 24 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POU2AF2	NM_198498.3	c.164-729A>T		intron_variant	Intron 3 of 4	ENST00000280325.7	NP_940900.2
POU2AF2	XM_011542804.3	c.98-729A>T		intron_variant	Intron 2 of 3		XP_011541106.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POU2AF2	ENST00000280325.7	c.164-729A>T		intron_variant	Intron 3 of 4	5	NM_198498.3	ENSP00000280325.6
POU2AF2	ENST00000637637.1	c.8-729A>T		intron_variant	Intron 2 of 3	1		ENSP00000489630.1
POU2AF2	ENST00000635886.1	n.121-729A>T		intron_variant	Intron 2 of 3	5		ENSP00000489980.1
POU2AF2	ENST00000667535.1	n.154-729A>T		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes Cov.: 30

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

GnomAD4 genome Cov.: 30

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.47
DANN	Benign	0.13
PhyloP100		-0.79

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: rs7130173; hg19: chr11-111154072;