1-167264237-G-A

Variant names:

• chr1-167264237-G-A
• rs4657652
• NM_002697.4:c.61+43279G>A

Variant summary

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

The NM_002697.4(POU2F1):​c.61+43279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.398 in 151,126 control chromosomes in the GnomAD database, including 14,698 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 0.40 (14698 hom., cov: 29)
• Consequence: POU2F1 NM_002697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85
• Publications: 7 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]

LOC124900412 (HGNC:):

ACMG classification

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

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 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.61+43279G>A		intron	N/A	NP_002688.3
	POU2F1	NM_001365848.1		c.-304+22627G>A		intron	N/A	NP_001352777.1	A0A8A2IE78
	POU2F1	NM_001365849.1		c.-304+43279G>A		intron	N/A	NP_001352778.1	A0A8A2IE78

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU2F1	ENST00000367866.7	TSL:1 MANE Select	c.61+43279G>A		intron	N/A	ENSP00000356840.2	P14859-6
	POU2F1	ENST00000541643.7	TSL:1	c.-109-39237G>A		intron	N/A	ENSP00000441285.2	P14859-1
	POU2F1	ENST00000271411.8	TSL:1	n.62-39237G>A		intron	N/A	ENSP00000271411.5	Q16075

Frequencies

GnomAD3 genomes AF: 0.398 AC: 60155 AN: 151012 Hom.: 14683 Cov.: 29

Gnomad AFR AF: 0.115

Gnomad AMI AF: 0.581

Gnomad AMR AF: 0.528

Gnomad ASJ AF: 0.330

Gnomad EAS AF: 0.712

Gnomad SAS AF: 0.622

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.323

Gnomad NFE AF: 0.474

Gnomad OTH AF: 0.400

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

GnomAD4 genome AF: 0.398 AC: 60183 AN: 151126 Hom.: 14698 Cov.: 29 AF XY: 0.412 AC XY: 30370 AN XY: 73788

African (AFR) AF: 0.115 AC: 4725 AN: 41126

American (AMR) AF: 0.528 AC: 8032 AN: 15204

Ashkenazi Jewish (ASJ) AF: 0.330 AC: 1136 AN: 3446

East Asian (EAS) AF: 0.713 AC: 3669 AN: 5146

South Asian (SAS) AF: 0.621 AC: 2980 AN: 4796

European-Finnish (FIN) AF: 0.586 AC: 6061 AN: 10344

Middle Eastern (MID) AF: 0.330 AC: 97 AN: 294

European-Non Finnish (NFE) AF: 0.474 AC: 32100 AN: 67758

Other (OTH) AF: 0.407 AC: 857 AN: 2106

Alfa AF: 0.445 Hom.: 20144

Bravo AF: 0.383

Asia WGS AF: 0.645 AC: 2243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
CADD	Benign	0.55
DANN	Benign	0.78
PhyloP100		-1.8
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: rs4657652; hg19: chr1-167233474;