Genetic Variant PHF3:c.407-9_407-8delCT (chr6-63684119-CCT-C) – ACMG Classification: Benign (-9 pts)

Variant summary

Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP6BS1BS2

The NM_001370348.2(PHF3):c.407-9_407-8delCT variant causes a splice region, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0135 in 1,563,428 control chromosomes in the GnomAD database, including 170 homozygotes. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.010 ( 14 hom., cov: 32)

Exomes 𝑓: 0.014 ( 156 hom. )

Consequence

PHF3
NM_001370348.2 splice_region, intron

Scores

Not classified

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: 2.10

Variant links:

Genes affected

PHF3 (HGNC:8921): (PHD finger protein 3) This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

PHF3 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -9 ACMG points.

BP6

Variant 6-63684119-CCT-C is Benign according to our data. Variant chr6-63684119-CCT-C is described in ClinVar as [Benign]. Clinvar id is 3037746.Status of the report is no_assertion_criteria_provided, 0 stars.

BS1

Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00999 (1518/152008) while in subpopulation NFE AF= 0.0159 (1077/67938). AF 95% confidence interval is 0.0151. There are 14 homozygotes in gnomad4. There are 742 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.

BS2

High Homozygotes in GnomAd4 at 14 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF3	NM_001370348.2 link	c.407-9_407-8delCT		splice_region_variant, intron_variant	Intron 3 of 15	ENST00000262043.8	NP_001357277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF3	ENST00000262043.8 link	c.407-9_407-8delCT		splice_region_variant, intron_variant	Intron 3 of 15	5	NM_001370348.2	ENSP00000262043.4		Q92576-1

Frequencies

GnomAD3 genomes

AF:

0.0100

AC:

1519

AN:

151890

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00319

Gnomad AMI

AF:

0.00329

Gnomad AMR

AF:

0.00420

Gnomad ASJ

AF:

0.00894

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.0189

Gnomad MID

AF:

0.00316

Gnomad NFE

AF:

0.0159

Gnomad OTH

AF:

0.00527

GnomAD3 exomes

AF:

0.00993

AC:

2141

AN:

215666

Hom.:

AF XY:

0.00994

AC XY:

1166

AN XY:

117342

show subpopulations

Gnomad AFR exome

AF:

0.00189

Gnomad AMR exome

AF:

0.00231

Gnomad ASJ exome

AF:

0.0100

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.0168

Gnomad NFE exome

AF:

0.0156

Gnomad OTH exome

AF:

0.00721

GnomAD4 exome

AF:

0.0139

AC:

19647

AN:

1411420

Hom.:

156

AF XY:

0.0135

AC XY:

9459

AN XY:

700386

show subpopulations

Gnomad4 AFR exome

AF:

0.00149

Gnomad4 AMR exome

AF:

0.00247

Gnomad4 ASJ exome

AF:

0.00910

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000889

Gnomad4 FIN exome

AF:

0.0159

Gnomad4 NFE exome

AF:

0.0164

Gnomad4 OTH exome

AF:

0.0101

GnomAD4 genome

AF:

0.00999

AC:

1518

AN:

152008

Hom.:

Cov.:

AF XY:

0.00998

AC XY:

742

AN XY:

74324

show subpopulations

Gnomad4 AFR

AF:

0.00318

Gnomad4 AMR

AF:

0.00419

Gnomad4 ASJ

AF:

0.00894

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.0189

Gnomad4 NFE

AF:

0.0159

Gnomad4 OTH

AF:

0.00521

Alfa

AF:

0.0110

Hom.:

Bravo

AF:

0.00830

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: no assertion criteria provided

LINK: link

Submissions by phenotype

PHF3-related disorder

Benign:1

Sep 05, 2019

PreventionGenetics, part of Exact Sciences

Significance: Benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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