Variant chr13-49506711-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BA1

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 (no stars).

Frequency

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

Exomes 𝑓: 0.67 ( 328653 hom. )

Consequence

PHF11
NM_001040443.3 synonymous

Scores

Clinical Significance

Benign no assertion criteria provided 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]

PHF11 links:

SETDB2-PHF11 (HGNC:):

SETDB2-PHF11 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.87).

BP6

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 no_assertion_criteria_provided, 0 stars.

BP7

Synonymous conserved (PhyloP=0.108 with no splicing effect.

BA1

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
PHF11	NM_001040443.3 linkuse as main transcript	c.171A>G	p.Leu57=	synonymous_variant	2/10	ENST00000378319.8
SETDB2-PHF11	NR_135324.2 linkuse as main transcript	n.2663-6348A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF11	ENST00000378319.8 linkuse as main transcript	c.171A>G	p.Leu57=	synonymous_variant	2/10	1	NM_001040443.3	P2	Q9UIL8-1

Frequencies

GnomAD3 genomes

AF:

0.729

AC:

110659

AN:

151798

Hom.:

41259

Cov.:

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.:

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

AF:

0.729

AC:

110780

AN:

151916

Hom.:

41321

Cov.:

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: no assertion criteria provided

LINK: link

Submissions by phenotype

PHF11-related disorder

Benign:1

Benign, no assertion criteria provided

clinical testing

PreventionGenetics, part of Exact Sciences

Oct 17, 2019

This 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.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over