NM_002697.4:c.62-51627C>T

Variant names:

• chr1-167280843-C-T
• rs7532692
• NM_002697.4:c.62-51627C>T

Variant summary

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

The NM_002697.4(POU2F1):​c.62-51627C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.169 in 152,086 control chromosomes in the GnomAD database, including 2,312 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 0.17 (2312 hom., cov: 33)
• Consequence: POU2F1 NM_002697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0450
• Publications: 6 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=-0.53).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.197 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POU2F1	NM_002697.4	c.62-51627C>T		intron_variant	Intron 1 of 15	ENST00000367866.7	NP_002688.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POU2F1	ENST00000367866.7	c.62-51627C>T		intron_variant	Intron 1 of 15	1	NM_002697.4	ENSP00000356840.2

Frequencies

GnomAD3 genomes AF: 0.169 AC: 25686 AN: 151968 Hom.: 2313 Cov.: 33

Gnomad AFR AF: 0.132

Gnomad AMI AF: 0.213

Gnomad AMR AF: 0.145

Gnomad ASJ AF: 0.194

Gnomad EAS AF: 0.134

Gnomad SAS AF: 0.104

Gnomad FIN AF: 0.186

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.179

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

GnomAD4 genome AF: 0.169 AC: 25684 AN: 152086 Hom.: 2312 Cov.: 33 AF XY: 0.166 AC XY: 12311 AN XY: 74336

African (AFR) AF: 0.131 AC: 5451 AN: 41478

American (AMR) AF: 0.145 AC: 2218 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.194 AC: 672 AN: 3472

East Asian (EAS) AF: 0.133 AC: 690 AN: 5174

South Asian (SAS) AF: 0.104 AC: 501 AN: 4818

European-Finnish (FIN) AF: 0.186 AC: 1963 AN: 10548

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

European-Non Finnish (NFE) AF: 0.200 AC: 13577 AN: 67988

Other (OTH) AF: 0.177 AC: 374 AN: 2114

Alfa AF: 0.188 Hom.: 8416

Bravo AF: 0.164

Asia WGS AF: 0.135 AC: 470 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.53
CADD	Benign	9.3
DANN	Benign	0.78
PhyloP100		0.045
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: rs7532692; hg19: chr1-167250080;