chr1-167223667-G-A

Variant names:

• chr1-167223667-G-A
• rs1497862
• NM_002697.4:c.61+2709G>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+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
• 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=-0.89).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.974 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+2709G>A		intron	N/A	NP_002688.3
	POU2F1	NM_001365848.1		c.-508+2709G>A		intron	N/A	NP_001352777.1	A0A8A2IE78
	POU2F1	NM_001365849.1		c.-304+2709G>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+2709G>A		intron	N/A	ENSP00000356840.2	P14859-6
	POU2F1	ENST00000541643.7	TSL:1	c.-110+2709G>A		intron	N/A	ENSP00000441285.2	P14859-1
	POU2F1	ENST00000271411.8	TSL:1	n.61+2709G>A		intron	N/A	ENSP00000271411.5	Q16075

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

African (AFR) AF: 0.727 AC: 30091 AN: 41416

American (AMR) AF: 0.963 AC: 14733 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.966 AC: 3349 AN: 3468

East Asian (EAS) AF: 0.997 AC: 5175 AN: 5190

South Asian (SAS) AF: 0.968 AC: 4668 AN: 4820

European-Finnish (FIN) AF: 0.985 AC: 10438 AN: 10602

Middle Eastern (MID) AF: 0.969 AC: 285 AN: 294

European-Non Finnish (NFE) AF: 0.980 AC: 66697 AN: 68036

Other (OTH) AF: 0.942 AC: 1989 AN: 2112

Alfa AF: 0.941 Hom.: 29470

Bravo AF: 0.899

Asia WGS AF: 0.975 AC: 3390 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.052
DANN	Benign	0.68
PhyloP100		-0.022
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs1497862; hg19: chr1-167192904;