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GeneBe

13-49506711-A-G

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_001040443.3(PHF11):c.171A>G(p.Leu57=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.675 in 1,605,470 control chromosomes in the GnomAD database, including 369,974 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.73 ( 41321 hom., cov: 30)
Exomes 𝑓: 0.67 ( 328653 hom. )

Consequence

PHF11
NM_001040443.3 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.108
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.87).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 13-49506711-A-G is Benign according to our data. Variant chr13-49506711-A-G is described in ClinVar as [Benign]. Clinvar id is 3059044.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=0.108 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.869 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
PHF11NM_001040443.3 linkuse as main transcriptc.171A>G p.Leu57= synonymous_variant 2/10 ENST00000378319.8
SETDB2-PHF11NR_135324.2 linkuse as main transcriptn.2663-6348A>G intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
PHF11ENST00000378319.8 linkuse as main transcriptc.171A>G p.Leu57= synonymous_variant 2/101 NM_001040443.3 P2Q9UIL8-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.729
AC:
110659
AN:
151798
Hom.:
41259
Cov.:
30
show subpopulations
Gnomad AFR
AF:
0.876
Gnomad AMI
AF:
0.523
Gnomad AMR
AF:
0.741
Gnomad ASJ
AF:
0.591
Gnomad EAS
AF:
0.870
Gnomad SAS
AF:
0.667
Gnomad FIN
AF:
0.673
Gnomad MID
AF:
0.671
Gnomad NFE
AF:
0.650
Gnomad OTH
AF:
0.705
GnomAD3 exomes
AF:
0.704
AC:
176593
AN:
250890
Hom.:
63108
AF XY:
0.693
AC XY:
93990
AN XY:
135636
show subpopulations
Gnomad AFR exome
AF:
0.884
Gnomad AMR exome
AF:
0.777
Gnomad ASJ exome
AF:
0.608
Gnomad EAS exome
AF:
0.861
Gnomad SAS exome
AF:
0.654
Gnomad FIN exome
AF:
0.687
Gnomad NFE exome
AF:
0.657
Gnomad OTH exome
AF:
0.677
GnomAD4 exome
AF:
0.669
AC:
972541
AN:
1453554
Hom.:
328653
Cov.:
30
AF XY:
0.668
AC XY:
483382
AN XY:
723660
show subpopulations
Gnomad4 AFR exome
AF:
0.882
Gnomad4 AMR exome
AF:
0.767
Gnomad4 ASJ exome
AF:
0.611
Gnomad4 EAS exome
AF:
0.894
Gnomad4 SAS exome
AF:
0.646
Gnomad4 FIN exome
AF:
0.681
Gnomad4 NFE exome
AF:
0.653
Gnomad4 OTH exome
AF:
0.682
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.729
AC:
110780
AN:
151916
Hom.:
41321
Cov.:
30
AF XY:
0.730
AC XY:
54242
AN XY:
74260
show subpopulations
Gnomad4 AFR
AF:
0.876
Gnomad4 AMR
AF:
0.742
Gnomad4 ASJ
AF:
0.591
Gnomad4 EAS
AF:
0.870
Gnomad4 SAS
AF:
0.667
Gnomad4 FIN
AF:
0.673
Gnomad4 NFE
AF:
0.650
Gnomad4 OTH
AF:
0.702
Alfa
AF:
0.663
Hom.:
57612
Bravo
AF:
0.741
Asia WGS
AF:
0.764
AC:
2659
AN:
3478
EpiCase
AF:
0.654
EpiControl
AF:
0.644

ClinVar

Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

PHF11-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 17, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.87
Cadd
Benign
0.88
Dann
Benign
0.55

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs2031532; hg19: chr13-50080847; COSMIC: COSV62896216; API