dbSNP rs222851: PHF23:c.997+11C>T (chr17-7235919-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_024297.3(PHF23):c.997+11C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.407 in 1,610,124 control chromosomes in the GnomAD database, including 137,148 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 0.45 ( 16233 hom., cov: 33)

Exomes 𝑓: 0.40 ( 120915 hom. )

Consequence

PHF23
NM_024297.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.169

Publications

29 publications found

Variant links:

Genes affected

PHF23 (HGNC:28428): (PHD finger protein 23) Predicted to enable metal ion binding activity. Involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of protein ubiquitination. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

PHF23 links:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.88).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.609 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF23	NM_024297.3 link	c.997+11C>T		intron_variant	Intron 4 of 4	ENST00000320316.8	NP_077273.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF23	ENST00000320316.8 link	c.997+11C>T		intron_variant	Intron 4 of 4	1	NM_024297.3	ENSP00000322579.3

Frequencies

GnomAD3 genomes

AF:

0.452

AC:

68635

AN:

152000

Hom.:

16225

Cov.:

show subpopulations

Gnomad AFR

AF:

0.591

Gnomad AMI

AF:

0.405

Gnomad AMR

AF:

0.445

Gnomad ASJ

AF:

0.428

Gnomad EAS

AF:

0.626

Gnomad SAS

AF:

0.374

Gnomad FIN

AF:

0.357

Gnomad MID

AF:

0.278

Gnomad NFE

AF:

0.379

Gnomad OTH

AF:

0.416

GnomAD2 exomes

AF:

0.423

AC:

104528

AN:

246890

AF XY:

0.411

show subpopulations

Gnomad AFR exome

AF:

0.598

Gnomad AMR exome

AF:

0.508

Gnomad ASJ exome

AF:

0.419

Gnomad EAS exome

AF:

0.623

Gnomad FIN exome

AF:

0.359

Gnomad NFE exome

AF:

0.373

Gnomad OTH exome

AF:

0.401

GnomAD4 exome

AF:

0.402

AC:

586098

AN:

1458006

Hom.:

120915

Cov.:

AF XY:

0.398

AC XY:

288528

AN XY:

724506

show subpopulations

African (AFR)

AF:

0.599

AC:

20020

AN:

33418

American (AMR)

AF:

0.499

AC:

22274

AN:

44632

Ashkenazi Jewish (ASJ)

AF:

0.415

AC:

10784

AN:

25978

East Asian (EAS)

AF:

0.652

AC:

25836

AN:

39606

South Asian (SAS)

AF:

0.359

AC:

30944

AN:

86154

European-Finnish (FIN)

AF:

0.366

AC:

19501

AN:

53342

Middle Eastern (MID)

AF:

0.320

AC:

1839

AN:

5752

European-Non Finnish (NFE)

AF:

0.387

AC:

429571

AN:

1108896

Other (OTH)

AF:

0.421

AC:

25329

AN:

60228

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

23382

46765

70147

93530

116912

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

13838

27676

41514

55352

69190

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.451

AC:

68676

AN:

152118

Hom.:

16233

Cov.:

AF XY:

0.448

AC XY:

33317

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.591

AC:

24514

AN:

41486

American (AMR)

AF:

0.445

AC:

6802

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.428

AC:

1487

AN:

3472

East Asian (EAS)

AF:

0.627

AC:

3245

AN:

5178

South Asian (SAS)

AF:

0.371

AC:

1789

AN:

4822

European-Finnish (FIN)

AF:

0.357

AC:

3778

AN:

10584

Middle Eastern (MID)

AF:

0.276

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.379

AC:

25745

AN:

67976

Other (OTH)

AF:

0.410

AC:

866

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1904

3808

5713

7617

9521

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

612

1224

1836

2448

3060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.393

Hom.:

11270

Bravo

AF:

0.469

Asia WGS

AF:

0.481

AC:

1671

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.88

CADD

Benign

(source)

DANN

Benign

0.85

PhyloP100

0.17

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over