rs6932538

chr6-63673079-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370348.2(PHF3):c.245-6921C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.545 in 151,550 control chromosomes in the GnomAD database, including 24,044 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 0.55 (24044 hom., cov: 30)
• Consequence: PHF3 NM_001370348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.653

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.75 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF3	NM_001370348.2	c.245-6921C>T		intron_variant		ENST00000262043.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF3	ENST00000262043.8	c.245-6921C>T		intron_variant		5	NM_001370348.2	P1

Frequencies

GnomAD3 genomes AF: 0.545 AC: 82497 AN: 151436 Hom.: 23991 Cov.: 30

Gnomad AFR AF: 0.757

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.559

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.562

Gnomad FIN AF: 0.360

Gnomad MID AF: 0.475

Gnomad NFE AF: 0.454

Gnomad OTH AF: 0.507

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.545 AC: 82607 AN: 151550 Hom.: 24044 Cov.: 30 AF XY: 0.543 AC XY: 40185 AN XY: 74006

Gnomad4 AFR AF: 0.757

Gnomad4 AMR AF: 0.559

Gnomad4 ASJ AF: 0.473

Gnomad4 EAS AF: 0.445

Gnomad4 SAS AF: 0.563

Gnomad4 FIN AF: 0.360

Gnomad4 NFE AF: 0.454

Gnomad4 OTH AF: 0.503

Alfa AF: 0.512 Hom.: 3116

Bravo AF: 0.569

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
Cadd	Benign	0.88
Dann	Benign	0.13

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

Other links and lift over

dbSNP: rs6932538; hg19: chr6-64382980;