Genetic Variant PHF11:c.769+24G>A (chr13-49524240-G-A) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The NM_001040443.3(PHF11):c.769+24G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000764 in 1,558,914 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00071 ( 0 hom., cov: 31)

Exomes 𝑓: 0.00077 ( 0 hom. )

Consequence

PHF11
NM_001040443.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.0290

Publications

11 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

ACMG classification

Classification was made for transcript

Our verdict: Likely_benign. The variant received -4 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.85).

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
PHF11	NM_001040443.3	MANE Select	c.769+24G>A	intron	N/A	NP_001035533.1
SETDB2-PHF11	NM_001320727.2		c.2251+24G>A	intron	N/A	NP_001307656.1
PHF11	NM_001040444.3		c.652+24G>A	intron	N/A	NP_001035534.1

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein
PHF11	ENST00000378319.8	TSL:1 MANE Select	c.769+24G>A	intron	N/A	ENSP00000367570.3
PHF11	ENST00000488958.5	TSL:1	c.652+24G>A	intron	N/A	ENSP00000417539.1
PHF11	ENST00000465045.5	TSL:1	n.652+24G>A	intron	N/A	ENSP00000418630.1

Frequencies

GnomAD3 genomes

AF:

0.000712

AC:

107

AN:

150284

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000978

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000998

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00468

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000886

Gnomad OTH

AF:

0.00194

GnomAD2 exomes

AF:

0.000746

AC:

170

AN:

227738

AF XY:

0.000724

show subpopulations

Gnomad AFR exome

AF:

0.000207

Gnomad AMR exome

AF:

0.000249

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00484

Gnomad FIN exome

AF:

0.0000472

Gnomad NFE exome

AF:

0.000735

Gnomad OTH exome

AF:

0.000365

GnomAD4 exome

AF:

0.000770

AC:

1084

AN:

1408516

Hom.:

Cov.:

AF XY:

0.000745

AC XY:

523

AN XY:

702310

show subpopulations

African (AFR)

AF:

0.0000642

AC:

AN:

31176

American (AMR)

AF:

0.000429

AC:

AN:

39588

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

25376

East Asian (EAS)

AF:

0.00159

AC:

AN:

38276

South Asian (SAS)

AF:

0.0000123

AC:

AN:

81164

European-Finnish (FIN)

AF:

0.0000382

AC:

AN:

52406

Middle Eastern (MID)

AF:

0.00

AC:

AN:

4958

European-Non Finnish (NFE)

AF:

0.000873

AC:

940

AN:

1077314

Other (OTH)

AF:

0.00105

AC:

AN:

58258

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.477

Heterozygous variant carriers

128

170

213

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

102

136

170

<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:

0.000711

AC:

107

AN:

150398

Hom.:

Cov.:

AF XY:

0.000723

AC XY:

AN XY:

73264

show subpopulations

African (AFR)

AF:

0.0000975

AC:

AN:

41026

American (AMR)

AF:

0.000997

AC:

AN:

15052

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3464

East Asian (EAS)

AF:

0.00469

AC:

AN:

5112

South Asian (SAS)

AF:

0.00

AC:

AN:

4774

European-Finnish (FIN)

AF:

0.00

AC:

AN:

9994

Middle Eastern (MID)

AF:

0.00

AC:

AN:

288

European-Non Finnish (NFE)

AF:

0.000886

AC:

AN:

67696

Other (OTH)

AF:

0.00192

AC:

AN:

2084

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.496

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<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:

0.0000166

Hom.:

1255

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

4.6

(source)

DANN

Benign

0.88

PhyloP100

0.029

Mutation Taster

=100/0

polymorphism

(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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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