1-167389282-A-G

Position:

• chr1-167389282-A-G

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POU2F1	NM_002697.4	c.814-306A>G		intron_variant		ENST00000367866.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU2F1	ENST00000367866.7	c.814-306A>G		intron_variant		1	NM_002697.4	A1

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

Gnomad4 AFR AF: 0.0776

Gnomad4 AMR AF: 0.142

Gnomad4 ASJ AF: 0.191

Gnomad4 EAS AF: 0.156

Gnomad4 SAS AF: 0.115

Gnomad4 FIN AF: 0.186

Gnomad4 NFE AF: 0.203

Gnomad4 OTH AF: 0.167

Alfa AF: 0.170 Hom.: 280

Bravo AF: 0.149

Asia WGS AF: 0.140 AC: 488 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	8.6
DANN	Benign	0.83

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: rs12117962; hg19: chr1-167358519;