Genetic Variant PHF3:c.244+23_244+33dupTTTTTTTTTTT (chr6-63646806-C-CTTTTTTTTTTT) – ACMG Classification: Uncertain_significance (0 pts)

Variant summary

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

The NM_001370348.2(PHF3):c.244+23_244+33dupTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.000024 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

PHF3
NM_001370348.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 1.19

Publications

1 publications found

Variant links:

Genes affected

PHF3 (HGNC:8921): (PHD finger protein 3) This gene encodes a member of a PHD finger-containing gene family. This gene may function as a transcription factor and may be involved in glioblastomas development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2014]

PHF3 links:

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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_001370348.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PHF3	NM_001370348.2	MANE Select	c.244+23_244+33dupTTTTTTTTTTT	intron	N/A	NP_001357277.1	Q92576-1
PHF3	NM_015153.4		c.244+23_244+33dupTTTTTTTTTTT	intron	N/A	NP_055968.1	Q92576-1
PHF3	NM_001290259.2		c.-214+23_-214+33dupTTTTTTTTTTT	intron	N/A	NP_001277188.1	Q92576-2

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
PHF3	ENST00000262043.8	TSL:5 MANE Select	c.244+11_244+12insTTTTTTTTTTT	intron	N/A	ENSP00000262043.4	Q92576-1
PHF3	ENST00000393387.5	TSL:1	c.244+11_244+12insTTTTTTTTTTT	intron	N/A	ENSP00000377048.1	Q92576-1
PHF3	ENST00000506783.5	TSL:1	c.-153+10656_-153+10657insTTTTTTTTTTT	intron	N/A	ENSP00000424694.1	E7EVH3

Frequencies

GnomAD3 genomes

AF:

0.0000235

AC:

AN:

85068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000466

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:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.0000231

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

928472

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

442354

African (AFR)

AF:

0.00

AC:

AN:

19272

American (AMR)

AF:

0.00

AC:

AN:

9848

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

12030

East Asian (EAS)

AF:

0.00

AC:

AN:

22996

South Asian (SAS)

AF:

0.00

AC:

AN:

18570

European-Finnish (FIN)

AF:

0.00

AC:

AN:

19366

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2434

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

787138

Other (OTH)

AF:

0.00

AC:

AN:

36818

GnomAD4 genome

AF:

0.0000235

AC:

AN:

85068

Hom.:

Cov.:

AF XY:

0.0000255

AC XY:

AN XY:

39158

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0000466

AC:

AN:

21442

American (AMR)

AF:

0.00

AC:

AN:

8056

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2376

East Asian (EAS)

AF:

0.00

AC:

AN:

2974

South Asian (SAS)

AF:

0.00

AC:

AN:

2316

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2732

Middle Eastern (MID)

AF:

0.00

AC:

AN:

128

European-Non Finnish (NFE)

AF:

0.0000231

AC:

AN:

43308

Other (OTH)

AF:

0.00

AC:

AN:

1096

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.250

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Alfa

AF:

0.000964

Hom.:

238

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

PhyloP100

1.2

Splicing

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

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over