rs1497862

chr1-167223667-G-Achr1-167223667-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_002697.4(POU2F1):c.61+2709G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.909 in 152,146 control chromosomes in the GnomAD database, including 63,841 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 0.91 (63841 hom., cov: 30)
• Consequence: POU2F1 NM_002697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0220

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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POU2F1	NM_002697.4	c.61+2709G>A		intron_variant		ENST00000367866.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU2F1	ENST00000367866.7	c.61+2709G>A		intron_variant		1	NM_002697.4	A1

Frequencies

GnomAD3 genomes AF: 0.909 AC: 138255 AN: 152028 Hom.: 63815 Cov.: 30

Gnomad AFR AF: 0.727

Gnomad AMI AF: 0.996

Gnomad AMR AF: 0.963

Gnomad ASJ AF: 0.966

Gnomad EAS AF: 0.997

Gnomad SAS AF: 0.968

Gnomad FIN AF: 0.985

Gnomad MID AF: 0.968

Gnomad NFE AF: 0.980

Gnomad OTH AF: 0.941

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

GnomAD4 genome AF: 0.909 AC: 138331 AN: 152146 Hom.: 63841 Cov.: 30 AF XY: 0.912 AC XY: 67826 AN XY: 74386

Gnomad4 AFR AF: 0.727

Gnomad4 AMR AF: 0.963

Gnomad4 ASJ AF: 0.966

Gnomad4 EAS AF: 0.997

Gnomad4 SAS AF: 0.968

Gnomad4 FIN AF: 0.985

Gnomad4 NFE AF: 0.980

Gnomad4 OTH AF: 0.942

Alfa AF: 0.941 Hom.: 17958

Bravo AF: 0.899

Asia WGS AF: 0.975 AC: 3390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
Cadd	Benign	0.052
Dann	Benign	0.68

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		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: rs1497862; hg19: chr1-167192904;