rs10258862

chr7-39077198-T-C

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001370959.1(POU6F2):c.106-8662T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.332 in 152,064 control chromosomes in the GnomAD database, including 8,618 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 0.33 (8618 hom., cov: 32)
• Consequence: POU6F2 NM_001370959.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.361

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.28).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.437 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
POU6F2	NM_001370959.1	c.106-8662T>C		intron_variant		ENST00000518318.7
POU6F2	NM_001166018.2	c.19-8662T>C		intron_variant
POU6F2	NM_007252.4	c.19-8662T>C		intron_variant
POU6F2	XM_047419843.1	c.19-8662T>C		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
POU6F2	ENST00000518318.7	c.106-8662T>C		intron_variant		1	NM_001370959.1	P2

Frequencies

GnomAD3 genomes AF: 0.332 AC: 50475 AN: 151944 Hom.: 8615 Cov.: 32

Gnomad AFR AF: 0.365

Gnomad AMI AF: 0.227

Gnomad AMR AF: 0.371

Gnomad ASJ AF: 0.356

Gnomad EAS AF: 0.124

Gnomad SAS AF: 0.452

Gnomad FIN AF: 0.339

Gnomad MID AF: 0.424

Gnomad NFE AF: 0.309

Gnomad OTH AF: 0.341

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

GnomAD4 genome AF: 0.332 AC: 50493 AN: 152064 Hom.: 8618 Cov.: 32 AF XY: 0.334 AC XY: 24834 AN XY: 74338

Gnomad4 AFR AF: 0.364

Gnomad4 AMR AF: 0.371

Gnomad4 ASJ AF: 0.356

Gnomad4 EAS AF: 0.124

Gnomad4 SAS AF: 0.453

Gnomad4 FIN AF: 0.339

Gnomad4 NFE AF: 0.309

Gnomad4 OTH AF: 0.335

Alfa AF: 0.321 Hom.: 7805

Bravo AF: 0.330

Asia WGS AF: 0.279 AC: 969 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.28
Cadd	Benign	18
Dann	Benign	0.83

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: rs10258862; hg19: chr7-39116798;