rs4657652

chr1-167264237-G-Achr1-167264237-G-Cchr1-167264237-G-T

Variant summary

Our verdict is Benign. Variant got -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

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=-0.78).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.694 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POU2F1	NM_002697.4	c.61+43279G>A		intron_variant		ENST00000367866.7
LOC124900412	XR_007066718.1	n.20190G>A		non_coding_transcript_exon_variant	2/2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU2F1	ENST00000367866.7	c.61+43279G>A		intron_variant		1	NM_002697.4	A1

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

Gnomad4 AFR AF: 0.115

Gnomad4 AMR AF: 0.528

Gnomad4 ASJ AF: 0.330

Gnomad4 EAS AF: 0.713

Gnomad4 SAS AF: 0.621

Gnomad4 FIN AF: 0.586

Gnomad4 NFE AF: 0.474

Gnomad4 OTH AF: 0.407

Alfa AF: 0.458 Hom.: 16445

Bravo AF: 0.383

Asia WGS AF: 0.645 AC: 2243 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.78
Cadd	Benign	0.55
Dann	Benign	0.78

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: rs4657652; hg19: chr1-167233474;