Genetic Variant PHF11:c.94+33_94+36delCGGG (chr13-49496108-GGGGC-G) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001419873.1(PHF11):c.-506_-503delCGGG variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.535 in 691,168 control chromosomes in the GnomAD database, including 136,139 homozygotes. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.71 ( 37995 hom., cov: 0)

Exomes 𝑓: 0.49 ( 98144 hom. )

Consequence

PHF11
NM_001419873.1 5_prime_UTR

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0640

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 -10 ACMG points.

BP6

Variant 13-49496108-GGGGC-G is Benign according to our data. Variant chr13-49496108-GGGGC-G is described in ClinVar as [Benign]. Clinvar id is 2975967.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.791 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF11	NM_001040443.3 link	c.94+33_94+36delCGGG		intron_variant	Intron 1 of 9	ENST00000378319.8	NP_001035533.1	Q9UIL8-1B4DDL5

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF11	ENST00000378319.8 link	c.94+14_94+17delGGGC		intron_variant	Intron 1 of 9	1	NM_001040443.3	ENSP00000367570.3		Q9UIL8-1

Frequencies

GnomAD3 genomes

AF:

0.710

AC:

106375

AN:

149862

Hom.:

37957

Cov.:

show subpopulations

Gnomad AFR

AF:

0.672

Gnomad AMI

AF:

0.717

Gnomad AMR

AF:

0.743

Gnomad ASJ

AF:

0.715

Gnomad EAS

AF:

0.811

Gnomad SAS

AF:

0.607

Gnomad FIN

AF:

0.783

Gnomad MID

AF:

0.708

Gnomad NFE

AF:

0.713

Gnomad OTH

AF:

0.725

GnomAD3 exomes

AF:

0.0426

AC:

AN:

Hom.:

AF XY:

0.0645

AC XY:

AN XY:

show subpopulations

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad SAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.105

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.487

AC:

263521

AN:

541196

Hom.:

98144

AF XY:

0.501

AC XY:

134315

AN XY:

267862

show subpopulations

Gnomad4 AFR exome

AF:

0.473

Gnomad4 AMR exome

AF:

0.719

Gnomad4 ASJ exome

AF:

0.645

Gnomad4 EAS exome

AF:

0.844

Gnomad4 SAS exome

AF:

0.461

Gnomad4 FIN exome

AF:

0.770

Gnomad4 NFE exome

AF:

0.442

Gnomad4 OTH exome

AF:

0.553

GnomAD4 genome

AF:

0.710

AC:

106455

AN:

149972

Hom.:

37995

Cov.:

AF XY:

0.712

AC XY:

52123

AN XY:

73158

show subpopulations

Gnomad4 AFR

AF:

0.672

Gnomad4 AMR

AF:

0.744

Gnomad4 ASJ

AF:

0.715

Gnomad4 EAS

AF:

0.812

Gnomad4 SAS

AF:

0.607

Gnomad4 FIN

AF:

0.783

Gnomad4 NFE

AF:

0.713

Gnomad4 OTH

AF:

0.722

Asia WGS

AF:

0.673

AC:

2279

AN:

3390

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Oct 02, 2024

Labcorp Genetics (formerly Invitae), Labcorp

Significance: Benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

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