rs3767434

Variant names:

• chr1-167401914-T-C
• rs3767434
• NM_002697.4:c.1555+358T>C

Variant summary

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

The NM_002697.4(POU2F1):​c.1555+358T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,284 control chromosomes in the GnomAD database, including 1,901 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 0.14 (1901 hom., cov: 32)
• Consequence: POU2F1 NM_002697.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.111
• Publications: 5 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=-0.86).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.198 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
POU2F1	NM_002697.4	c.1555+358T>C		intron_variant	Intron 13 of 15	ENST00000367866.7	NP_002688.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
POU2F1	ENST00000367866.7	c.1555+358T>C		intron_variant	Intron 13 of 15	1	NM_002697.4	ENSP00000356840.2

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21865 AN: 152166 Hom.: 1902 Cov.: 32

Gnomad AFR AF: 0.0516

Gnomad AMI AF: 0.214

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.191

Gnomad EAS AF: 0.139

Gnomad SAS AF: 0.106

Gnomad FIN AF: 0.145

Gnomad MID AF: 0.134

Gnomad NFE AF: 0.200

Gnomad OTH AF: 0.159

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

GnomAD4 genome AF: 0.144 AC: 21857 AN: 152284 Hom.: 1901 Cov.: 32 AF XY: 0.140 AC XY: 10436 AN XY: 74460

African (AFR) AF: 0.0515 AC: 2139 AN: 41572

American (AMR) AF: 0.137 AC: 2088 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.191 AC: 663 AN: 3470

East Asian (EAS) AF: 0.139 AC: 719 AN: 5188

South Asian (SAS) AF: 0.106 AC: 510 AN: 4820

European-Finnish (FIN) AF: 0.145 AC: 1533 AN: 10602

Middle Eastern (MID) AF: 0.137 AC: 40 AN: 292

European-Non Finnish (NFE) AF: 0.201 AC: 13639 AN: 68020

Other (OTH) AF: 0.157 AC: 331 AN: 2114

Alfa AF: 0.170 Hom.: 683

Bravo AF: 0.138

Asia WGS AF: 0.133 AC: 463 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	1.3
DANN	Benign	0.50
PhyloP100		-0.11
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: rs3767434; hg19: chr1-167371151;