Variant chr13-49528674-G-A details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BA1

The NM_001040443.3(PHF11):c.*9G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.512 in 1,573,548 control chromosomes in the GnomAD database, including 209,815 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (no stars).

Frequency

Genomes: 𝑓 0.48 ( 17652 hom., cov: 32)

Exomes 𝑓: 0.52 ( 192163 hom. )

Consequence

PHF11
NM_001040443.3 3_prime_UTR

Scores

Clinical Significance

Benign no assertion criteria provided B:1

Conservation

PhyloP100: -1.28

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 -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BP6

Variant 13-49528674-G-A is Benign according to our data. Variant chr13-49528674-G-A is described in ClinVar as [Benign]. Clinvar id is 3059533.Status of the report is no_assertion_criteria_provided, 0 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.528 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.*9G>A		3_prime_UTR_variant	10/10	ENST00000378319.8
SETDB2-PHF11	NR_135324.2 linkuse as main transcript	n.3616G>A		non_coding_transcript_exon_variant	21/21

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF11	ENST00000378319.8 linkuse as main transcript	c.*9G>A		3_prime_UTR_variant	10/10	1	NM_001040443.3	P2	Q9UIL8-1

Frequencies

GnomAD3 genomes

AF:

0.476

AC:

72294

AN:

151872

Hom.:

17641

Cov.:

show subpopulations

Gnomad AFR

AF:

0.365

Gnomad AMI

AF:

0.432

Gnomad AMR

AF:

0.521

Gnomad ASJ

AF:

0.541

Gnomad EAS

AF:

0.467

Gnomad SAS

AF:

0.320

Gnomad FIN

AF:

0.528

Gnomad MID

AF:

0.598

Gnomad NFE

AF:

0.533

Gnomad OTH

AF:

0.506

GnomAD3 exomes

AF:

0.496

AC:

112360

AN:

226708

Hom.:

28392

AF XY:

0.491

AC XY:

60336

AN XY:

122778

show subpopulations

Gnomad AFR exome

AF:

0.361

Gnomad AMR exome

AF:

0.533

Gnomad ASJ exome

AF:

0.567

Gnomad EAS exome

AF:

0.478

Gnomad SAS exome

AF:

0.319

Gnomad FIN exome

AF:

0.541

Gnomad NFE exome

AF:

0.534

Gnomad OTH exome

AF:

0.530

GnomAD4 exome

AF:

0.515

AC:

732671

AN:

1421560

Hom.:

192163

Cov.:

AF XY:

0.511

AC XY:

361893

AN XY:

707694

show subpopulations

Gnomad4 AFR exome

AF:

0.360

Gnomad4 AMR exome

AF:

0.523

Gnomad4 ASJ exome

AF:

0.565

Gnomad4 EAS exome

AF:

0.492

Gnomad4 SAS exome

AF:

0.316

Gnomad4 FIN exome

AF:

0.535

Gnomad4 NFE exome

AF:

0.533

Gnomad4 OTH exome

AF:

0.511

GnomAD4 genome

AF:

0.476

AC:

72339

AN:

151988

Hom.:

17652

Cov.:

AF XY:

0.473

AC XY:

35114

AN XY:

74276

show subpopulations

Gnomad4 AFR

AF:

0.365

Gnomad4 AMR

AF:

0.521

Gnomad4 ASJ

AF:

0.541

Gnomad4 EAS

AF:

0.468

Gnomad4 SAS

AF:

0.319

Gnomad4 FIN

AF:

0.528

Gnomad4 NFE

AF:

0.533

Gnomad4 OTH

AF:

0.503

Alfa

AF:

0.524

Hom.:

22368

Bravo

AF:

0.476

Asia WGS

AF:

0.389

AC:

1351

AN:

3478

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

-0.95

CADD

Benign

0.58

DANN

Benign

0.56

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