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

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP6_ModerateBA1

The NM_001040443.3(PHF11):c.94+33_94+36delCGGG variant causes a intron 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_001040443.3 intron

Scores

Not classified

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.0640

Publications

1 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:

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ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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

GnomAD2 exomes

AF:

0.0426

AC:

AN:

AF XY:

0.0645

show subpopulations

Gnomad AMR exome

AF:

0.00

Gnomad ASJ 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

African (AFR)

AF:

0.473

AC:

5518

AN:

11672

American (AMR)

AF:

0.719

AC:

5024

AN:

6986

Ashkenazi Jewish (ASJ)

AF:

0.645

AC:

6726

AN:

10424

East Asian (EAS)

AF:

0.844

AC:

18374

AN:

21766

South Asian (SAS)

AF:

0.461

AC:

10299

AN:

22344

European-Finnish (FIN)

AF:

0.770

AC:

18115

AN:

23522

Middle Eastern (MID)

AF:

0.584

AC:

1035

AN:

1772

European-Non Finnish (NFE)

AF:

0.442

AC:

184431

AN:

417388

Other (OTH)

AF:

0.553

AC:

13999

AN:

25322

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.552

Heterozygous variant carriers

3075

6150

9226

12301

15376

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.710

AC:

106455

AN:

149972

Hom.:

37995

Cov.:

AF XY:

0.712

AC XY:

52123

AN XY:

73158

show subpopulations

African (AFR)

AF:

0.672

AC:

27532

AN:

40950

American (AMR)

AF:

0.744

AC:

11287

AN:

15170

Ashkenazi Jewish (ASJ)

AF:

0.715

AC:

2478

AN:

3464

East Asian (EAS)

AF:

0.812

AC:

3980

AN:

4904

South Asian (SAS)

AF:

0.607

AC:

2892

AN:

4764

European-Finnish (FIN)

AF:

0.783

AC:

7946

AN:

10150

Middle Eastern (MID)

AF:

0.707

AC:

205

AN:

290

European-Non Finnish (NFE)

AF:

0.713

AC:

47985

AN:

67296

Other (OTH)

AF:

0.722

AC:

1510

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.522

Heterozygous variant carriers

1542

3085

4627

6170

7712

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.607

Hom.:

1272

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

PhyloP100

0.064

Mutation Taster

=100/0

polymorphism (auto)

(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

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13-49496108-GGGGC-G

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

Other links and lift over