rs6932538

Variant names:

• chr6-63673079-C-T
• rs6932538
• NM_001370348.2:c.245-6921C>T

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -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.

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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF3	NM_001370348.2	MANE Select	c.245-6921C>T		intron	N/A	NP_001357277.1
	PHF3	NM_015153.4		c.245-6921C>T		intron	N/A	NP_055968.1
	PHF3	NM_001290259.2		c.-213-5749C>T		intron	N/A	NP_001277188.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF3	ENST00000262043.8	TSL:5 MANE Select	c.245-6921C>T		intron	N/A	ENSP00000262043.4
	PHF3	ENST00000393387.5	TSL:1	c.245-6921C>T		intron	N/A	ENSP00000377048.1
	PHF3	ENST00000506783.5	TSL:1	c.-152-11050C>T		intron	N/A	ENSP00000424694.1

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

African (AFR) AF: 0.757 AC: 31250 AN: 41290

American (AMR) AF: 0.559 AC: 8515 AN: 15220

Ashkenazi Jewish (ASJ) AF: 0.473 AC: 1640 AN: 3468

East Asian (EAS) AF: 0.445 AC: 2285 AN: 5140

South Asian (SAS) AF: 0.563 AC: 2702 AN: 4800

European-Finnish (FIN) AF: 0.360 AC: 3761 AN: 10452

Middle Eastern (MID) AF: 0.486 AC: 142 AN: 292

European-Non Finnish (NFE) AF: 0.454 AC: 30806 AN: 67876

Other (OTH) AF: 0.503 AC: 1058 AN: 2102

Alfa AF: 0.519 Hom.: 3323

Bravo AF: 0.569

Asia WGS AF: 0.479 AC: 1664 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	0.88
DANN	Benign	0.13
PhyloP100		-0.65
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs6932538; hg19: chr6-64382980;