1-167287553-T-C

Variant summary

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

The NM_002697.4(POU2F1):c.62-44917T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.107 in 152,240 control chromosomes in the GnomAD database, including 2,162 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 0.11 (2162 hom., cov: 32)
• Consequence: POU2F1 NM_002697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.511

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

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.315 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POU2F1	NM_002697.4	c.62-44917T>C		intron_variant		ENST00000367866.7
LOC124900412	XR_007066718.1	n.43506T>C		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU2F1	ENST00000367866.7	c.62-44917T>C		intron_variant		1	NM_002697.4	A1

Frequencies

GnomAD3 genomes AF: 0.107 AC: 16237 AN: 152122 Hom.: 2151 Cov.: 32

Gnomad AFR AF: 0.319

Gnomad AMI AF: 0.00439

Gnomad AMR AF: 0.0470

Gnomad ASJ AF: 0.0351

Gnomad EAS AF: 0.00288

Gnomad SAS AF: 0.0321

Gnomad FIN AF: 0.0347

Gnomad MID AF: 0.0443

Gnomad NFE AF: 0.0220

Gnomad OTH AF: 0.0746

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

GnomAD4 genome AF: 0.107 AC: 16284 AN: 152240 Hom.: 2162 Cov.: 32 AF XY: 0.105 AC XY: 7801 AN XY: 74428

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.0468

Gnomad4 ASJ AF: 0.0351

Gnomad4 EAS AF: 0.00289

Gnomad4 SAS AF: 0.0319

Gnomad4 FIN AF: 0.0347

Gnomad4 NFE AF: 0.0220

Gnomad4 OTH AF: 0.0739

Alfa AF: 0.0218 Hom.: 31

Bravo AF: 0.118

Asia WGS AF: 0.0300 AC: 105 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
Cadd	Benign	0.68
Dann	Benign	0.63

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: rs266819; hg19: chr1-167256790;