rs3757350

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_001370348.2(PHF3):​c.-25-2785A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0782 in 152,284 control chromosomes in the GnomAD database, including 537 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.078 ( 537 hom., cov: 32)

Consequence

PHF3
NM_001370348.2 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.622
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.85).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.155 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
PHF3NM_001370348.2 linkuse as main transcriptc.-25-2785A>G intron_variant ENST00000262043.8 NP_001357277.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
PHF3ENST00000262043.8 linkuse as main transcriptc.-25-2785A>G intron_variant 5 NM_001370348.2 ENSP00000262043.4 Q92576-1

Frequencies

GnomAD3 genomes
AF:
0.0781
AC:
11884
AN:
152166
Hom.:
535
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0485
Gnomad AMI
AF:
0.0943
Gnomad AMR
AF:
0.0946
Gnomad ASJ
AF:
0.0579
Gnomad EAS
AF:
0.164
Gnomad SAS
AF:
0.0679
Gnomad FIN
AF:
0.123
Gnomad MID
AF:
0.0475
Gnomad NFE
AF:
0.0812
Gnomad OTH
AF:
0.0607
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.0781
AC:
11901
AN:
152284
Hom.:
537
Cov.:
32
AF XY:
0.0809
AC XY:
6024
AN XY:
74456
show subpopulations
Gnomad4 AFR
AF:
0.0486
Gnomad4 AMR
AF:
0.0951
Gnomad4 ASJ
AF:
0.0579
Gnomad4 EAS
AF:
0.164
Gnomad4 SAS
AF:
0.0679
Gnomad4 FIN
AF:
0.123
Gnomad4 NFE
AF:
0.0812
Gnomad4 OTH
AF:
0.0591
Alfa
AF:
0.0770
Hom.:
673
Bravo
AF:
0.0771
Asia WGS
AF:
0.0930
AC:
325
AN:
3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.85
CADD
Benign
4.1
DANN
Benign
0.59

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3757350; hg19: chr6-64353647; API