Genetic Variant PHF3:c.244+21_244+33delTTTTTTTTTTTTT (chr6-63646806-CTTTTTTTTTTTTT-C) – 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+21_244+33delTTTTTTTTTTTTT variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000316 in 1,013,540 control chromosomes in the GnomAD database, with no homozygous occurrence. It is difficult to determine the true allele frequency of this variant because it is of type DEL_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 0.000035 ( 0 hom., cov: 0)

Exomes 𝑓: 0.000031 ( 0 hom. )

Consequence

PHF3
NM_001370348.2 intron

Scores

Not classified

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.23

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+21_244+33delTTTTTTTTTTTTT	intron	N/A	NP_001357277.1	Q92576-1
PHF3	NM_015153.4		c.244+21_244+33delTTTTTTTTTTTTT	intron	N/A	NP_055968.1	Q92576-1
PHF3	NM_001290259.2		c.-214+21_-214+33delTTTTTTTTTTTTT	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+12_244+24delTTTTTTTTTTTTT	intron	N/A	ENSP00000262043.4	Q92576-1
PHF3	ENST00000393387.5	TSL:1	c.244+12_244+24delTTTTTTTTTTTTT	intron	N/A	ENSP00000377048.1	Q92576-1
PHF3	ENST00000506783.5	TSL:1	c.-153+10657_-153+10669delTTTTTTTTTTTTT	intron	N/A	ENSP00000424694.1	E7EVH3

Frequencies

GnomAD3 genomes

AF:

0.0000353

AC:

AN:

85068

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.000124

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:

0.0000462

Gnomad OTH

AF:

0.00

GnomAD4 exome

AF:

0.0000312

AC:

AN:

928472

Hom.:

AF XY:

0.0000362

AC XY:

AN XY:

442354

show subpopulations

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:

0.0000318

AC:

AN:

787138

Other (OTH)

AF:

0.000109

AC:

AN:

36818

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.551

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:

0.0000353

AC:

AN:

85068

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

39158

show subpopulations

African (AFR)

AF:

0.00

AC:

AN:

21442

American (AMR)

AF:

0.000124

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:

0.0000462

AC:

AN:

43308

Other (OTH)

AF:

0.00

AC:

AN:

1096

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.442

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

3.2

Splicing

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

Publications

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6-63646806-CTTTTTTTTTTTTTT-CT

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