Genetic Variant PHF11:c.217-53T>C (chr13-49513006-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_001040443.3(PHF11):c.217-53T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.276 in 851,258 control chromosomes in the GnomAD database, including 34,490 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 0.24 ( 5030 hom., cov: 32)

Exomes 𝑓: 0.28 ( 29460 hom. )

Consequence

PHF11
NM_001040443.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.42

Publications

17 publications found

Variant links:

Genes affected

PHF11 (HGNC:17024): (PHD finger protein 11) This gene encodes a protein containing a PHD (plant homeodomain) type zinc finger. This gene has been identified in some studies as a candidate gene for asthma. Naturally-occurring readthrough transcription may occur from the upstream SETDB2 (SET domain bifurcated 2) gene to this locus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]

PHF11 links:

SETDB2-PHF11 (HGNC:):

SETDB2-PHF11 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001040443.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.362 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040443.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PHF11	NM_001040443.3	MANE Select	c.217-53T>C	intron	N/A	NP_001035533.1	Q9UIL8-1
SETDB2-PHF11	NM_001320727.2		c.1699-53T>C	intron	N/A	NP_001307656.1
PHF11	NM_001040444.3		c.100-53T>C	intron	N/A	NP_001035534.1	Q9UIL8-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PHF11	ENST00000378319.8	TSL:1 MANE Select	c.217-53T>C	intron	N/A	ENSP00000367570.3	Q9UIL8-1
PHF11	ENST00000488958.5	TSL:1	c.100-53T>C	intron	N/A	ENSP00000417539.1	Q9UIL8-2
PHF11	ENST00000465045.5	TSL:1	n.100-53T>C	intron	N/A	ENSP00000418630.1	J3KR57

Frequencies

GnomAD3 genomes

AF:

0.239

AC:

36352

AN:

152020

Hom.:

5029

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0981

Gnomad AMI

AF:

0.215

Gnomad AMR

AF:

0.320

Gnomad ASJ

AF:

0.286

Gnomad EAS

AF:

0.375

Gnomad SAS

AF:

0.186

Gnomad FIN

AF:

0.231

Gnomad MID

AF:

0.376

Gnomad NFE

AF:

0.298

Gnomad OTH

AF:

0.276

GnomAD4 exome

AF:

0.284

AC:

198735

AN:

699120

Hom.:

29460

AF XY:

0.281

AC XY:

104529

AN XY:

371988

show subpopulations

African (AFR)

AF:

0.0942

AC:

1548

AN:

16440

American (AMR)

AF:

0.335

AC:

10234

AN:

30536

Ashkenazi Jewish (ASJ)

AF:

0.301

AC:

5593

AN:

18590

East Asian (EAS)

AF:

0.371

AC:

12262

AN:

33018

South Asian (SAS)

AF:

0.187

AC:

11357

AN:

60702

European-Finnish (FIN)

AF:

0.237

AC:

12004

AN:

50732

Middle Eastern (MID)

AF:

0.322

AC:

1328

AN:

4120

European-Non Finnish (NFE)

AF:

0.299

AC:

134586

AN:

450414

Other (OTH)

AF:

0.284

AC:

9823

AN:

34568

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

6575

13149

19724

26298

32873

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2386

4772

7158

9544

11930

<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:

0.239

AC:

36348

AN:

152138

Hom.:

5030

Cov.:

AF XY:

0.238

AC XY:

17696

AN XY:

74390

show subpopulations

African (AFR)

AF:

0.0978

AC:

4063

AN:

41528

American (AMR)

AF:

0.319

AC:

4882

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.286

AC:

991

AN:

3468

East Asian (EAS)

AF:

0.375

AC:

1938

AN:

5162

South Asian (SAS)

AF:

0.187

AC:

901

AN:

4826

European-Finnish (FIN)

AF:

0.231

AC:

2440

AN:

10582

Middle Eastern (MID)

AF:

0.373

AC:

109

AN:

292

European-Non Finnish (NFE)

AF:

0.298

AC:

20251

AN:

67974

Other (OTH)

AF:

0.273

AC:

577

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1374

2748

4122

5496

6870

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

378

756

1134

1512

1890

<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:

0.281

Hom.:

7008

Bravo

AF:

0.247

Asia WGS

AF:

0.259

AC:

897

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

0.036

(source)

DANN

Benign

0.57

PhyloP100

-1.4

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over