Genetic Variant PHF11:c.505+51A>G (chr13-49520991-A-G) – 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.505+51A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.509 in 1,500,974 control chromosomes in the GnomAD database, including 199,620 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 ( 16699 hom., cov: 33)

Exomes 𝑓: 0.51 ( 182921 hom. )

Consequence

PHF11
NM_001040443.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.09

Publications

13 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:

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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=-0.73).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.535 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF11	NM_001040443.3 link	c.505+51A>G		intron_variant	Intron 5 of 9	ENST00000378319.8	NP_001035533.1	Q9UIL8-1B4DDL5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8 link	c.505+51A>G		intron_variant	Intron 5 of 9	1	NM_001040443.3	ENSP00000367570.3		Q9UIL8-1

Frequencies

GnomAD3 genomes

AF:

0.454

AC:

68953

AN:

151924

Hom.:

16689

Cov.:

show subpopulations

Gnomad AFR

AF:

0.280

Gnomad AMI

AF:

0.434

Gnomad AMR

AF:

0.510

Gnomad ASJ

AF:

0.483

Gnomad EAS

AF:

0.482

Gnomad SAS

AF:

0.316

Gnomad FIN

AF:

0.534

Gnomad MID

AF:

0.561

Gnomad NFE

AF:

0.540

Gnomad OTH

AF:

0.482

GnomAD2 exomes

AF:

0.489

AC:

105261

AN:

215366

AF XY:

0.486

show subpopulations

Gnomad AFR exome

AF:

0.272

Gnomad AMR exome

AF:

0.527

Gnomad ASJ exome

AF:

0.507

Gnomad EAS exome

AF:

0.492

Gnomad FIN exome

AF:

0.543

Gnomad NFE exome

AF:

0.539

Gnomad OTH exome

AF:

0.510

GnomAD4 exome

AF:

0.515

AC:

694666

AN:

1348932

Hom.:

182921

Cov.:

AF XY:

0.511

AC XY:

343151

AN XY:

671642

show subpopulations

African (AFR)

AF:

0.274

AC:

8234

AN:

30016

American (AMR)

AF:

0.517

AC:

17150

AN:

33194

Ashkenazi Jewish (ASJ)

AF:

0.504

AC:

12011

AN:

23836

East Asian (EAS)

AF:

0.501

AC:

19315

AN:

38544

South Asian (SAS)

AF:

0.306

AC:

22835

AN:

74646

European-Finnish (FIN)

AF:

0.538

AC:

28083

AN:

52198

Middle Eastern (MID)

AF:

0.495

AC:

2691

AN:

5434

European-Non Finnish (NFE)

AF:

0.537

AC:

556188

AN:

1035002

Other (OTH)

AF:

0.502

AC:

28159

AN:

56062

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

14032

28064

42097

56129

70161

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

15510

31020

46530

62040

77550

<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:

0.454

AC:

68981

AN:

152042

Hom.:

16699

Cov.:

AF XY:

0.452

AC XY:

33566

AN XY:

74308

show subpopulations

African (AFR)

AF:

0.279

AC:

11584

AN:

41470

American (AMR)

AF:

0.510

AC:

7796

AN:

15274

Ashkenazi Jewish (ASJ)

AF:

0.483

AC:

1676

AN:

3468

East Asian (EAS)

AF:

0.482

AC:

2497

AN:

5180

South Asian (SAS)

AF:

0.316

AC:

1526

AN:

4826

European-Finnish (FIN)

AF:

0.534

AC:

5627

AN:

10540

Middle Eastern (MID)

AF:

0.568

AC:

166

AN:

292

European-Non Finnish (NFE)

AF:

0.540

AC:

36703

AN:

67974

Other (OTH)

AF:

0.480

AC:

1011

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1837

3675

5512

7350

9187

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

622

1244

1866

2488

3110

<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:

0.496

Hom.:

3714

Bravo

AF:

0.451

Asia WGS

AF:

0.381

AC:

1322

AN:

3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.73

CADD

Benign

7.9

(source)

DANN

Benign

0.74

PhyloP100

1.1

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