Genetic Variant NM_001040443.3:c.94+33_94+36dupCGGG (chr13-49496108-G-GGGGC) – 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+33_94+36dupCGGG 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 0.00011 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000035 ( 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:

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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+33_94+36dupCGGG	intron	N/A	NP_001035533.1	Q9UIL8-1
PHF11	NM_001419873.1		c.-506_-503dupCGGG	5_prime_UTR	Exon 1 of 11	NP_001406802.1	Q9UIL8-2
PHF11	NM_001419874.1		c.-540_-537dupCGGG	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+14insGGGC	intron	N/A	ENSP00000367570.3	Q9UIL8-1
PHF11	ENST00000941732.1		c.94+13_94+14insGGGC	intron	N/A	ENSP00000611791.1
PHF11	ENST00000873990.1		c.94+13_94+14insGGGC	intron	N/A	ENSP00000544049.1

Frequencies

GnomAD3 genomes

AF:

0.000113

AC:

AN:

149918

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000735

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000198

Gnomad ASJ

AF:

0.000289

Gnomad EAS

AF:

0.000203

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.000134

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000351

AC:

AN:

541810

Hom.:

Cov.:

AF XY:

0.0000373

AC XY:

AN XY:

268156

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

11704

American (AMR)

AF:

0.000143

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:

0.00

AC:

AN:

22380

European-Finnish (FIN)

AF:

0.0000425

AC:

AN:

23544

Middle Eastern (MID)

AF:

0.000564

AC:

AN:

1774

European-Non Finnish (NFE)

AF:

0.0000311

AC:

AN:

417836

Other (OTH)

AF:

0.000118

AC:

AN:

25354

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.422

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:

0.000113

AC:

AN:

150028

Hom.:

Cov.:

AF XY:

0.000137

AC XY:

AN XY:

73184

show subpopulations

African (AFR)

AF:

0.0000732

AC:

AN:

40958

American (AMR)

AF:

0.000198

AC:

AN:

15180

Ashkenazi Jewish (ASJ)

AF:

0.000289

AC:

AN:

3464

East Asian (EAS)

AF:

0.000204

AC:

AN:

4910

South Asian (SAS)

AF:

0.00

AC:

AN:

4764

European-Finnish (FIN)

AF:

0.00

AC:

AN:

10154

Middle Eastern (MID)

AF:

0.00

AC:

AN:

290

European-Non Finnish (NFE)

AF:

0.000134

AC:

AN:

67324

Other (OTH)

AF:

0.00

AC:

AN:

2092

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

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:

0.000155

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