chr11-111283347-A-C

Variant names:

• chr11-111283347-A-C
• rs7130173
• NM_198498.3:c.164-729A>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.164-729A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.706 in 151,886 control chromosomes in the GnomAD database, including 38,004 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 0.71 (38004 hom., 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.804 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.164-729A>C		intron	N/A	NP_940900.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2AF2	ENST00000280325.7	TSL:5 MANE Select	c.164-729A>C		intron	N/A	ENSP00000280325.6
	POU2AF2	ENST00000637637.1	TSL:1	c.8-729A>C		intron	N/A	ENSP00000489630.1
	POU2AF2	ENST00000635886.1	TSL:5	n.121-729A>C		intron	N/A	ENSP00000489980.1

Frequencies

GnomAD3 genomes AF: 0.706 AC: 107129 AN: 151768 Hom.: 37965 Cov.: 30

Gnomad AFR AF: 0.647

Gnomad AMI AF: 0.549

Gnomad AMR AF: 0.776

Gnomad ASJ AF: 0.726

Gnomad EAS AF: 0.593

Gnomad SAS AF: 0.825

Gnomad FIN AF: 0.775

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.716

Gnomad OTH AF: 0.710

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

GnomAD4 genome AF: 0.706 AC: 107223 AN: 151886 Hom.: 38004 Cov.: 30 AF XY: 0.711 AC XY: 52726 AN XY: 74206

African (AFR) AF: 0.647 AC: 26778 AN: 41404

American (AMR) AF: 0.776 AC: 11853 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.726 AC: 2519 AN: 3470

East Asian (EAS) AF: 0.593 AC: 3055 AN: 5152

South Asian (SAS) AF: 0.825 AC: 3953 AN: 4790

European-Finnish (FIN) AF: 0.775 AC: 8155 AN: 10526

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.716 AC: 48662 AN: 67960

Other (OTH) AF: 0.715 AC: 1507 AN: 2108

Alfa AF: 0.687 Hom.: 17969

Bravo AF: 0.699

Asia WGS AF: 0.758 AC: 2634 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	0.49
DANN	Benign	0.20
PhyloP100		-0.79
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: rs7130173; hg19: chr11-111154072;