Genetic Variant PHF3:c.244+31_244+33dupTTT (chr6-63646806-C-CTTT) – 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+31_244+33dupTTT 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 0.000071 ( 0 hom., cov: 0)

Exomes 𝑓: 0.00035 ( 0 hom. )

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+31_244+33dupTTT	intron	N/A	NP_001357277.1	Q92576-1
PHF3	NM_015153.4		c.244+31_244+33dupTTT	intron	N/A	NP_055968.1	Q92576-1
PHF3	NM_001290259.2		c.-214+31_-214+33dupTTT	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+12insTTT	intron	N/A	ENSP00000262043.4	Q92576-1
PHF3	ENST00000393387.5	TSL:1	c.244+11_244+12insTTT	intron	N/A	ENSP00000377048.1	Q92576-1
PHF3	ENST00000506783.5	TSL:1	c.-153+10656_-153+10657insTTT	intron	N/A	ENSP00000424694.1	E7EVH3

Frequencies

GnomAD3 genomes

AF:

0.0000705

AC:

AN:

85058

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000140

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000124

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.000336

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

AF:

0.000348

AC:

323

AN:

927582

Hom.:

Cov.:

AF XY:

0.000310

AC XY:

137

AN XY:

441920

show subpopulations

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

African (AFR)

AF:

0.000467

AC:

AN:

19260

American (AMR)

AF:

0.000102

AC:

AN:

9846

Ashkenazi Jewish (ASJ)

AF:

0.000166

AC:

AN:

12020

East Asian (EAS)

AF:

0.000261

AC:

AN:

22984

South Asian (SAS)

AF:

0.000108

AC:

AN:

18556

European-Finnish (FIN)

AF:

0.000155

AC:

AN:

19360

Middle Eastern (MID)

AF:

0.00

AC:

AN:

2432

European-Non Finnish (NFE)

AF:

0.000369

AC:

290

AN:

786324

Other (OTH)

AF:

0.000272

AC:

AN:

36800

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 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: 0.251

Heterozygous variant carriers

127

169

211

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

100

<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:

0.0000706

AC:

AN:

85040

Hom.:

Cov.:

AF XY:

0.000102

AC XY:

AN XY:

39150

show subpopulations

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

African (AFR)

AF:

0.000140

AC:

AN:

21462

American (AMR)

AF:

0.000124

AC:

AN:

8054

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2374

East Asian (EAS)

AF:

0.000337

AC:

AN:

2964

South Asian (SAS)

AF:

0.00

AC:

AN:

2302

European-Finnish (FIN)

AF:

0.00

AC:

AN:

2732

Middle Eastern (MID)

AF:

0.00

AC:

AN:

118

European-Non Finnish (NFE)

AF:

0.0000231

AC:

AN:

43288

Other (OTH)

AF:

0.00

AC:

AN:

1106

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0.00000000000378308), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.292

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.:

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

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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