Genetic Variant NM_001040443.3:c.94+29_94+36dupCGGGCGGG (chr13-49496108-G-GGGGCGGGC) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001040443.3(PHF11):c.94+29_94+36dupCGGGCGGG variant causes a intron change involving the alteration of a non-conserved nucleotide. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000053 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

PHF11
NM_001040443.3 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

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:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript NM_001040443.3, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001040443.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PHF11	NM_001040443.3	MANE Select	c.94+29_94+36dupCGGGCGGG	intron	N/A	NP_001035533.1	Q9UIL8-1
PHF11	NM_001419873.1		c.-510_-503dupCGGGCGGG	5_prime_UTR	Exon 1 of 11	NP_001406802.1	Q9UIL8-2
PHF11	NM_001419874.1		c.-544_-537dupCGGGCGGG	5_prime_UTR	Exon 1 of 11	NP_001406803.1	Q9UIL8-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PHF11	ENST00000378319.8	TSL:1 MANE Select	c.94+13_94+14insGGGCGGGC	intron	N/A	ENSP00000367570.3	Q9UIL8-1
PHF11	ENST00000941732.1		c.94+13_94+14insGGGCGGGC	intron	N/A	ENSP00000611791.1
PHF11	ENST00000873990.1		c.94+13_94+14insGGGCGGGC	intron	N/A	ENSP00000544049.1

Frequencies

GnomAD3 genomes

AF:

0.0000534

AC:

AN:

149918

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000147

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.000197

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000185

AC:

AN:

541810

Hom.:

Cov.:

AF XY:

0.0000261

AC XY:

AN XY:

268156

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11704

American (AMR)

AF:

0.00

AC:

AN:

6992

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

10446

East Asian (EAS)

AF:

0.00

AC:

AN:

21780

South Asian (SAS)

AF:

0.0000447

AC:

AN:

22380

European-Finnish (FIN)

AF:

0.000212

AC:

AN:

23544

Middle Eastern (MID)

AF:

0.00

AC:

AN:

1774

European-Non Finnish (NFE)

AF:

0.00000957

AC:

AN:

417836

Other (OTH)

AF:

0.00

AC:

AN:

25354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.425

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.0000534

AC:

AN:

149918

Hom.:

Cov.:

AF XY:

0.0000684

AC XY:

AN XY:

73066

show subpopulations

African (AFR)

AF:

0.000147

AC:

AN:

40840

American (AMR)

AF:

0.00

AC:

AN:

15160

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

3464

East Asian (EAS)

AF:

0.00

AC:

AN:

4926

South Asian (SAS)

AF:

0.00

AC:

AN:

4766

European-Finnish (FIN)

AF:

0.000197

AC:

AN:

10154

Middle Eastern (MID)

AF:

0.00

AC:

AN:

312

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

67334

Other (OTH)

AF:

0.00

AC:

AN:

2070

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.444

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00

Hom.:

1272

Bravo

AF:

0.0000227

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

0.064

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over