rs12551314

Variant names:

• chr9-93617515-C-A
• rs12551314
• NM_005392.4:c.99-12455C>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PHF2	NM_005392.4	c.99-12455C>A		intron_variant	Intron 1 of 21	ENST00000359246.9	NP_005383.3
PHF2	XM_005252051.3	c.99-12455C>A		intron_variant	Intron 1 of 21		XP_005252108.1
PHF2	XM_006717143.3	c.99-12455C>A		intron_variant	Intron 1 of 21		XP_006717206.1
PHF2	XM_047423475.1	c.99-12455C>A		intron_variant	Intron 1 of 21		XP_047279431.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF2	ENST00000359246.9	c.99-12455C>A		intron_variant	Intron 1 of 21	1	NM_005392.4	ENSP00000352185.4
PHF2	ENST00000610682.1	c.99-12455C>A		intron_variant	Intron 1 of 7	5		ENSP00000479936.1

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

African (AFR) AF: 0.126 AC: 5249 AN: 41502

American (AMR) AF: 0.131 AC: 1998 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.133 AC: 460 AN: 3470

East Asian (EAS) AF: 0.198 AC: 1019 AN: 5156

South Asian (SAS) AF: 0.127 AC: 613 AN: 4822

European-Finnish (FIN) AF: 0.165 AC: 1744 AN: 10566

Middle Eastern (MID) AF: 0.0918 AC: 27 AN: 294

European-Non Finnish (NFE) AF: 0.125 AC: 8493 AN: 67986

Other (OTH) AF: 0.122 AC: 257 AN: 2110

Alfa AF: 0.127 Hom.: 2278

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
PhyloP100		-0.74
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: rs12551314; hg19: chr9-96379797;