rs12117962

Variant names:

• chr1-167389282-A-G
• rs12117962
• NM_002697.4:c.814-306A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002697.4(POU2F1):​c.814-306A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.156 in 152,234 control chromosomes in the GnomAD database, including 2,114 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 0.16 (2114 hom., cov: 32)
• Consequence: POU2F1 NM_002697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.73
• Publications: 0 publications found

Genes affected

POU2F1 (HGNC:9212): (POU class 2 homeobox 1) The OCT1 transcription factor was among the first identified members of the POU transcription factor family (summarized by Sturm et al., 1993 [PubMed 8314572]). Members of this family contain the POU domain, a 160-amino acid region necessary for DNA binding to the octameric sequence ATGCAAAT.[supplied by OMIM, Jul 2010]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_002697.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2F1	NM_002697.4	MANE Select	c.814-306A>G		intron	N/A	NP_002688.3
	POU2F1	NM_001198783.2		c.781-306A>G		intron	N/A	NP_001185712.1	P14859-2
	POU2F1	NM_001365848.1		c.739-306A>G		intron	N/A	NP_001352777.1	A0A8A2IE78

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2F1	ENST00000367866.7	TSL:1 MANE Select	c.814-306A>G		intron	N/A	ENSP00000356840.2	P14859-6
	POU2F1	ENST00000367862.9	TSL:1	c.781-306A>G		intron	N/A	ENSP00000356836.5	P14859-2
	POU2F1	ENST00000541643.7	TSL:1	c.745-306A>G		intron	N/A	ENSP00000441285.2	P14859-1

Frequencies

GnomAD3 genomes AF: 0.156 AC: 23771 AN: 152116 Hom.: 2113 Cov.: 32

Gnomad AFR AF: 0.0776

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.142

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.157

Gnomad SAS AF: 0.115

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.203

Gnomad OTH AF: 0.169

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

GnomAD4 genome AF: 0.156 AC: 23774 AN: 152234 Hom.: 2114 Cov.: 32 AF XY: 0.154 AC XY: 11486 AN XY: 74416

African (AFR) AF: 0.0776 AC: 3224 AN: 41558

American (AMR) AF: 0.142 AC: 2169 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 664 AN: 3470

East Asian (EAS) AF: 0.156 AC: 809 AN: 5186

South Asian (SAS) AF: 0.115 AC: 555 AN: 4824

European-Finnish (FIN) AF: 0.186 AC: 1972 AN: 10584

Middle Eastern (MID) AF: 0.153 AC: 45 AN: 294

European-Non Finnish (NFE) AF: 0.203 AC: 13789 AN: 68006

Other (OTH) AF: 0.167 AC: 352 AN: 2114

Alfa AF: 0.167 Hom.: 286

Bravo AF: 0.149

Asia WGS AF: 0.140 AC: 488 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.6
DANN	Benign	0.83
PhyloP100		1.7
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: rs12117962; hg19: chr1-167358519;