Genetic Variant PHF11:c.506-226C>G (chr13-49521817-C-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.506-226C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.543 in 301,792 control chromosomes in the GnomAD database, including 46,194 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 0.51 ( 20767 hom., cov: 32)

Exomes 𝑓: 0.57 ( 25427 hom. )

Consequence

PHF11
NM_001040443.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.11

Publications

7 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=-0.78).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.636 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.506-226C>G	intron	N/A	NP_001035533.1	Q9UIL8-1
SETDB2-PHF11	NM_001320727.2		c.1988-226C>G	intron	N/A	NP_001307656.1
PHF11	NM_001040444.3		c.389-226C>G	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.506-226C>G	intron	N/A	ENSP00000367570.3	Q9UIL8-1
PHF11	ENST00000488958.5	TSL:1	c.389-226C>G	intron	N/A	ENSP00000417539.1	Q9UIL8-2
PHF11	ENST00000465045.5	TSL:1	n.389-226C>G	intron	N/A	ENSP00000418630.1	J3KR57

Frequencies

GnomAD3 genomes

AF:

0.511

AC:

77612

AN:

151850

Hom.:

20742

Cov.:

show subpopulations

Gnomad AFR

AF:

0.350

Gnomad AMI

AF:

0.448

Gnomad AMR

AF:

0.561

Gnomad ASJ

AF:

0.531

Gnomad EAS

AF:

0.654

Gnomad SAS

AF:

0.445

Gnomad FIN

AF:

0.577

Gnomad MID

AF:

0.602

Gnomad NFE

AF:

0.580

Gnomad OTH

AF:

0.522

GnomAD4 exome

AF:

0.575

AC:

86083

AN:

149824

Hom.:

25427

AF XY:

0.569

AC XY:

44932

AN XY:

78910

show subpopulations

African (AFR)

AF:

0.344

AC:

1370

AN:

3982

American (AMR)

AF:

0.562

AC:

2142

AN:

3814

Ashkenazi Jewish (ASJ)

AF:

0.563

AC:

2869

AN:

5096

East Asian (EAS)

AF:

0.726

AC:

7193

AN:

9902

South Asian (SAS)

AF:

0.441

AC:

5430

AN:

12318

European-Finnish (FIN)

AF:

0.585

AC:

7755

AN:

13258

Middle Eastern (MID)

AF:

0.550

AC:

383

AN:

696

European-Non Finnish (NFE)

AF:

0.586

AC:

53764

AN:

91692

Other (OTH)

AF:

0.571

AC:

5177

AN:

9066

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.511

Heterozygous variant carriers

1750

3501

5251

7002

8752

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

198

396

594

792

990

<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:

0.511

AC:

77673

AN:

151968

Hom.:

20767

Cov.:

AF XY:

0.511

AC XY:

37957

AN XY:

74262

show subpopulations

African (AFR)

AF:

0.351

AC:

14539

AN:

41448

American (AMR)

AF:

0.561

AC:

8571

AN:

15268

Ashkenazi Jewish (ASJ)

AF:

0.531

AC:

1843

AN:

3470

East Asian (EAS)

AF:

0.654

AC:

3375

AN:

5158

South Asian (SAS)

AF:

0.446

AC:

2151

AN:

4818

European-Finnish (FIN)

AF:

0.577

AC:

6084

AN:

10552

Middle Eastern (MID)

AF:

0.606

AC:

177

AN:

292

European-Non Finnish (NFE)

AF:

0.580

AC:

39430

AN:

67944

Other (OTH)

AF:

0.519

AC:

1095

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1873

3747

5620

7494

9367

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

684

1368

2052

2736

3420

<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:

0.415

Hom.:

1178

Bravo

AF:

0.507

Asia WGS

AF:

0.512

AC:

1774

AN:

3472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.78

CADD

Benign

6.4

(source)

DANN

Benign

0.76

PhyloP100

2.1

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over