7-39081900-A-T

Variant names:

• chr7-39081900-A-T
• rs10464366
• NM_001370959.1:c.106-3960A>T

Variant summary

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

The NM_001370959.1(POU6F2):​c.106-3960A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,126 control chromosomes in the GnomAD database, including 5,168 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 0.24 (5168 hom., cov: 32)
• Consequence: POU6F2 NM_001370959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0690
• Publications: 6 publications found

Genes affected

POU6F2 (HGNC:21694): (POU class 6 homeobox 2) This gene encodes a member of the POU protein family characterized by the presence of a bipartite DNA binding domain, consisting of a POU-specific domain and a homeodomain, separated by a variable polylinker. The DNA binding domain may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner. The POU family members are transcriptional regulators, many of which are known to control cell type-specific differentiation pathways. This gene is a tumor suppressor involved in Wilms tumor (WT) predisposition. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene.[provided by RefSeq, Oct 2009]

POU6F2 Gene-Disease associations (from GenCC):

• Wilms tumor 5

  Inheritance: Unknown Classification: LIMITED Submitted by: Ambry Genetics

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 (EAS) allele frequency at 95% confidence interval = 0.709 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001370959.1. 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
	POU6F2	NM_001370959.1	MANE Select	c.106-3960A>T		intron	N/A	NP_001357888.1	A0A6E1XZL4
	POU6F2	NM_007252.4		c.19-3960A>T		intron	N/A	NP_009183.3	P78424-1
	POU6F2	NM_001166018.2		c.19-3960A>T		intron	N/A	NP_001159490.1	P78424-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	POU6F2	ENST00000518318.7	TSL:1 MANE Select	c.106-3960A>T		intron	N/A	ENSP00000430514.3	A0A6E1XZL4
	POU6F2	ENST00000403058.6	TSL:5	c.19-3960A>T		intron	N/A	ENSP00000384004.1	P78424-1
	POU6F2	ENST00000451021.5	TSL:4	n.158-3960A>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35815 AN: 152008 Hom.: 5168 Cov.: 32

Gnomad AFR AF: 0.136

Gnomad AMI AF: 0.215

Gnomad AMR AF: 0.288

Gnomad ASJ AF: 0.200

Gnomad EAS AF: 0.729

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.253

Gnomad MID AF: 0.127

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.218

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

GnomAD4 genome AF: 0.236 AC: 35827 AN: 152126 Hom.: 5168 Cov.: 32 AF XY: 0.242 AC XY: 17998 AN XY: 74366

African (AFR) AF: 0.136 AC: 5636 AN: 41516

American (AMR) AF: 0.288 AC: 4404 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.200 AC: 694 AN: 3468

East Asian (EAS) AF: 0.728 AC: 3754 AN: 5156

South Asian (SAS) AF: 0.269 AC: 1300 AN: 4828

European-Finnish (FIN) AF: 0.253 AC: 2683 AN: 10584

Middle Eastern (MID) AF: 0.123 AC: 36 AN: 292

European-Non Finnish (NFE) AF: 0.245 AC: 16662 AN: 67986

Other (OTH) AF: 0.218 AC: 462 AN: 2116

Alfa AF: 0.232 Hom.: 542

Bravo AF: 0.239

Asia WGS AF: 0.439 AC: 1523 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	3.0
DANN	Benign	0.65
PhyloP100		0.069
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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs10464366;

hg19: chr7-39121500;