Variant 9-93645638-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1

The NM_005392.4(PHF2):c.309C>T(p.Asp103Asp) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0818 in 1,597,282 control chromosomes in the GnomAD database, including 5,790 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.069 ( 433 hom., cov: 34)

Exomes 𝑓: 0.083 ( 5357 hom. )

Consequence

PHF2
NM_005392.4 synonymous

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.76

Variant links:

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]

PHF2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -21 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.57).

BP6

Variant 9-93645638-C-T is Benign according to our data. Variant chr9-93645638-C-T is described in ClinVar as [Benign]. Clinvar id is 1278335.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BP7

Synonymous conserved (PhyloP=-1.76 with no splicing effect.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.0862 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF2	NM_005392.4 link	c.309C>T	p.Asp103Asp	synonymous_variant	Exon 4 of 22	ENST00000359246.9	NP_005383.3	O75151

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	UniProt
PHF2	ENST00000359246.9 link	c.309C>T	p.Asp103Asp	synonymous_variant	Exon 4 of 22	1	NM_005392.4	ENSP00000352185.4	O75151
PHF2	ENST00000610682.1 link	c.239+9173C>T		intron_variant	Intron 3 of 7	5		ENSP00000479936.1	A0A087WW48
PHF2	ENST00000375376.8 link	c.187-7629C>T		intron_variant	Intron 3 of 8	5			E7ET14

Frequencies

GnomAD3 genomes

AF:

0.0691

AC:

10513

AN:

152200

Hom.:

431

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0435

Gnomad AMI

AF:

0.105

Gnomad AMR

AF:

0.0476

Gnomad ASJ

AF:

0.0403

Gnomad EAS

AF:

0.0634

Gnomad SAS

AF:

0.0371

Gnomad FIN

AF:

0.103

Gnomad MID

AF:

0.0443

Gnomad NFE

AF:

0.0881

Gnomad OTH

AF:

0.0630

GnomAD3 exomes

AF:

0.0703

AC:

16849

AN:

239700

Hom.:

730

AF XY:

0.0700

AC XY:

9048

AN XY:

129258

show subpopulations

Gnomad AFR exome

AF:

0.0419

Gnomad AMR exome

AF:

0.0320

Gnomad ASJ exome

AF:

0.0395

Gnomad EAS exome

AF:

0.0653

Gnomad SAS exome

AF:

0.0406

Gnomad FIN exome

AF:

0.0989

Gnomad NFE exome

AF:

0.0919

Gnomad OTH exome

AF:

0.0707

GnomAD4 exome

AF:

0.0832

AC:

120197

AN:

1444964

Hom.:

5357

Cov.:

AF XY:

0.0822

AC XY:

58941

AN XY:

717226

show subpopulations

Gnomad4 AFR exome

AF:

0.0434

Gnomad4 AMR exome

AF:

0.0323

Gnomad4 ASJ exome

AF:

0.0405

Gnomad4 EAS exome

AF:

0.0595

Gnomad4 SAS exome

AF:

0.0375

Gnomad4 FIN exome

AF:

0.0988

Gnomad4 NFE exome

AF:

0.0917

Gnomad4 OTH exome

AF:

0.0719

GnomAD4 genome

AF:

0.0691

AC:

10521

AN:

152318

Hom.:

433

Cov.:

AF XY:

0.0687

AC XY:

5116

AN XY:

74476

show subpopulations

Gnomad4 AFR

AF:

0.0436

Gnomad4 AMR

AF:

0.0474

Gnomad4 ASJ

AF:

0.0403

Gnomad4 EAS

AF:

0.0638

Gnomad4 SAS

AF:

0.0373

Gnomad4 FIN

AF:

0.103

Gnomad4 NFE

AF:

0.0881

Gnomad4 OTH

AF:

0.0638

Alfa

AF:

0.0753

Hom.:

308

Bravo

AF:

0.0659

Asia WGS

AF:

0.0660

AC:

227

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Breakthrough Genomics, Breakthrough Genomics

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: not provided

- -

Jun 13, 2019

GeneDx

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.57

CADD

Benign

1.8

DANN

Benign

0.66

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.8

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over