rs12551314

chr9-93617515-C-A

Variant summary

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

The NM_005392.4(PHF2):c.99-12455C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.133 in 152,108 control chromosomes in the GnomAD database, including 1,373 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 0.13 (1373 hom., cov: 32)
• Consequence: PHF2 NM_005392.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.738

Genes affected

PHF2 (HGNC:8920): (PHD finger protein 2) This gene encodes a protein which contains a zinc finger-like PHD (plant homeodomain) finger, distinct from other classes of zinc finger motifs, and a hydrophobic and highly conserved domain. The PHD finger shows the typical Cys4-His-Cys3 arrangement. PHD finger genes are thought to belong to a diverse group of transcriptional regulators possibly affecting eukaryotic gene expression by influencing chromatin structure. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.188 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF2	NM_005392.4	c.99-12455C>A		intron_variant		ENST00000359246.9
PHF2	XM_005252051.3	c.99-12455C>A		intron_variant
PHF2	XM_006717143.3	c.99-12455C>A		intron_variant
PHF2	XM_047423475.1	c.99-12455C>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF2	ENST00000359246.9	c.99-12455C>A		intron_variant		1	NM_005392.4	P1
PHF2	ENST00000610682.1	c.99-12455C>A		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.133 AC: 20162 AN: 151990 Hom.: 1366 Cov.: 32

Gnomad AFR AF: 0.126

Gnomad AMI AF: 0.359

Gnomad AMR AF: 0.130

Gnomad ASJ AF: 0.133

Gnomad EAS AF: 0.198

Gnomad SAS AF: 0.126

Gnomad FIN AF: 0.165

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.125

Gnomad OTH AF: 0.121

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

GnomAD4 genome AF: 0.133 AC: 20187 AN: 152108 Hom.: 1373 Cov.: 32 AF XY: 0.136 AC XY: 10082 AN XY: 74354

Gnomad4 AFR AF: 0.126

Gnomad4 AMR AF: 0.131

Gnomad4 ASJ AF: 0.133

Gnomad4 EAS AF: 0.198

Gnomad4 SAS AF: 0.127

Gnomad4 FIN AF: 0.165

Gnomad4 NFE AF: 0.125

Gnomad4 OTH AF: 0.122

Alfa AF: 0.125 Hom.: 1635

Bravo AF: 0.134

Asia WGS AF: 0.166 AC: 580 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.29
Dann	Benign	0.48

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: rs12551314; hg19: chr9-96379797;