Variant 6-63684165-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The NM_001370348.2(PHF3):c.443A>G(p.Lys148Arg) variant causes a missense change. The variant allele was found at a frequency of 0.00866 in 1,612,520 control chromosomes in the GnomAD database, including 100 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.0085 ( 10 hom., cov: 32)

Exomes 𝑓: 0.0087 ( 90 hom. )

Consequence

PHF3
NM_001370348.2 missense

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 4.43

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0066666007).

BP6

Variant 6-63684165-A-G is Benign according to our data. Variant chr6-63684165-A-G is described in ClinVar as [Benign]. Clinvar id is 781871.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAd4 at 10 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF3	NM_001370348.2 linkuse as main transcript	c.443A>G	p.Lys148Arg	missense_variant	4/16	ENST00000262043.8	NP_001357277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF3	ENST00000262043.8 linkuse as main transcript	c.443A>G	p.Lys148Arg	missense_variant	4/16	5	NM_001370348.2	ENSP00000262043	P1	Q92576-1

Frequencies

GnomAD3 genomes

AF:

0.00845

AC:

1286

AN:

152152

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00191

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00288

Gnomad ASJ

AF:

0.0360

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00290

Gnomad FIN

AF:

0.0338

Gnomad MID

AF:

0.0158

Gnomad NFE

AF:

0.00941

Gnomad OTH

AF:

0.00959

GnomAD3 exomes

AF:

0.00951

AC:

2374

AN:

249728

Hom.:

AF XY:

0.00930

AC XY:

1255

AN XY:

134978

show subpopulations

Gnomad AFR exome

AF:

0.00154

Gnomad AMR exome

AF:

0.00324

Gnomad ASJ exome

AF:

0.0382

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.00463

Gnomad FIN exome

AF:

0.0311

Gnomad NFE exome

AF:

0.00875

Gnomad OTH exome

AF:

0.00973

GnomAD4 exome

AF:

0.00868

AC:

12675

AN:

1460250

Hom.:

Cov.:

AF XY:

0.00867

AC XY:

6297

AN XY:

726392

show subpopulations

Gnomad4 AFR exome

AF:

0.00168

Gnomad4 AMR exome

AF:

0.00327

Gnomad4 ASJ exome

AF:

0.0364

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00448

Gnomad4 FIN exome

AF:

0.0305

Gnomad4 NFE exome

AF:

0.00789

Gnomad4 OTH exome

AF:

0.0109

GnomAD4 genome

AF:

0.00845

AC:

1287

AN:

152270

Hom.:

Cov.:

AF XY:

0.00925

AC XY:

689

AN XY:

74472

show subpopulations

Gnomad4 AFR

AF:

0.00190

Gnomad4 AMR

AF:

0.00288

Gnomad4 ASJ

AF:

0.0360

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00290

Gnomad4 FIN

AF:

0.0338

Gnomad4 NFE

AF:

0.00941

Gnomad4 OTH

AF:

0.00949

Alfa

AF:

0.00944

Hom.:

Bravo

AF:

0.00538

TwinsUK

AF:

0.00944

AC:

ALSPAC

AF:

0.00545

AC:

ESP6500AA

AF:

0.00136

AC:

ESP6500EA

AF:

0.00942

AC:

ExAC

AF:

0.00932

AC:

1132

Asia WGS

AF:

0.000577

AC:

AN:

3478

EpiCase

AF:

0.00797

EpiControl

AF:

0.00889

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Jun 08, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.12

BayesDel_addAF

Benign

-0.33

BayesDel_noAF

Benign

-0.23

CADD

Benign

DANN

Uncertain

1.0

DEOGEN2

Benign

0.064

T;T;T;.;T;.

Eigen

Pathogenic

0.71

Eigen_PC

Pathogenic

0.71

FATHMM_MKL

Pathogenic

0.97

LIST_S2

Benign

0.86

D;D;.;D;D;T

MetaRNN

Benign

0.0067

T;T;T;T;T;T

MetaSVM

Benign

-0.52

MutationAssessor

Benign

0.55

.;.;N;.;N;.

MutationTaster

Benign

1.0

D;D;D

PrimateAI

Uncertain

0.69

PROVEAN

Benign

-1.0

N;N;N;N;N;D

REVEL

Benign

0.18

Sift

Pathogenic

0.0

D;D;D;D;D;D

Sift4G

Uncertain

0.047

D;T;T;T;T;D

Polyphen

1.0

.;.;D;D;D;.

Vest4

0.46, 0.26, 0.61

MVP

0.56

MPC

0.30

ClinPred

0.036

GERP RS

5.9

Varity_R

0.33

gMVP

0.18

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.050

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