Genetic Variant NM_001370348.2:c.244+32_244+33dupTT (chr6-63646806-C-CTT) – 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+32_244+33dupTT 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 0.000059 ( 0 hom., cov: 0)

Exomes 𝑓: 0.0027 ( 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+32_244+33dupTT	intron	N/A	NP_001357277.1	Q92576-1
PHF3	NM_015153.4		c.244+32_244+33dupTT	intron	N/A	NP_055968.1	Q92576-1
PHF3	NM_001290259.2		c.-214+32_-214+33dupTT	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+12insTT	intron	N/A	ENSP00000262043.4	Q92576-1
PHF3	ENST00000393387.5	TSL:1	c.244+11_244+12insTT	intron	N/A	ENSP00000377048.1	Q92576-1
PHF3	ENST00000506783.5	TSL:1	c.-153+10656_-153+10657insTT	intron	N/A	ENSP00000424694.1	E7EVH3

Frequencies

GnomAD3 genomes

AF:

0.0000588

AC:

AN:

85064

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000187

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

GnomAD2 exomes

AF:

0.0000383

AC:

AN:

26084

AF XY:

0.00

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.0000666

Gnomad OTH exome

AF:

0.00

GnomAD4 exome

AF:

0.00271

AC:

2508

AN:

924634

Hom.:

Cov.:

AF XY:

0.00267

AC XY:

1176

AN XY:

440566

show subpopulations

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

African (AFR)

AF:

0.00271

AC:

AN:

19190

American (AMR)

AF:

0.000508

AC:

AN:

9834

Ashkenazi Jewish (ASJ)

AF:

0.00167

AC:

AN:

11992

East Asian (EAS)

AF:

0.00179

AC:

AN:

22916

South Asian (SAS)

AF:

0.00286

AC:

AN:

18502

European-Finnish (FIN)

AF:

0.00145

AC:

AN:

19328

Middle Eastern (MID)

AF:

0.00372

AC:

AN:

2420

European-Non Finnish (NFE)

AF:

0.00282

AC:

2209

AN:

783776

Other (OTH)

AF:

0.00248

AC:

AN:

36676

⚠️ 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: 0.262

Heterozygous variant carriers

276

553

829

1106

1382

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Variant carriers

102

204

306

408

510

<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:

0.0000588

AC:

AN:

85064

Hom.:

Cov.:

AF XY:

0.000102

AC XY:

AN XY:

39154

show subpopulations

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

African (AFR)

AF:

0.000187

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:

43304

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 = 0.000148522), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.335

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

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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