6-63676159-C-T

Variant names:

• chr6-63676159-C-T
• rs10485358
• NM_001370348.2:c.245-3841C>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.245-3841C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.553 in 151,996 control chromosomes in the GnomAD database, including 24,914 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 (24914 hom., cov: 32)
• Consequence: PHF3 NM_001370348.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.200
• Publications: 4 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=-0.95).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.77 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

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF3	NM_001370348.2	MANE Select	c.245-3841C>T		intron	N/A	NP_001357277.1	Q92576-1
	PHF3	NM_015153.4		c.245-3841C>T		intron	N/A	NP_055968.1	Q92576-1
	PHF3	NM_001290259.2		c.-213-2669C>T		intron	N/A	NP_001277188.1	Q92576-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF3	ENST00000262043.8	TSL:5 MANE Select	c.245-3841C>T		intron	N/A	ENSP00000262043.4	Q92576-1
	PHF3	ENST00000393387.5	TSL:1	c.245-3841C>T		intron	N/A	ENSP00000377048.1	Q92576-1
	PHF3	ENST00000506783.5	TSL:1	c.-152-7970C>T		intron	N/A	ENSP00000424694.1	E7EVH3

Frequencies

GnomAD3 genomes AF: 0.552 AC: 83866 AN: 151878 Hom.: 24857 Cov.: 32

Gnomad AFR AF: 0.776

Gnomad AMI AF: 0.491

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.473

Gnomad EAS AF: 0.445

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.359

Gnomad MID AF: 0.491

Gnomad NFE AF: 0.457

Gnomad OTH AF: 0.514

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

GnomAD4 genome AF: 0.553 AC: 83981 AN: 151996 Hom.: 24914 Cov.: 32 AF XY: 0.550 AC XY: 40849 AN XY: 74316

African (AFR) AF: 0.777 AC: 32197 AN: 41450

American (AMR) AF: 0.563 AC: 8593 AN: 15262

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

East Asian (EAS) AF: 0.445 AC: 2305 AN: 5178

South Asian (SAS) AF: 0.565 AC: 2723 AN: 4822

European-Finnish (FIN) AF: 0.359 AC: 3791 AN: 10558

Middle Eastern (MID) AF: 0.497 AC: 146 AN: 294

European-Non Finnish (NFE) AF: 0.457 AC: 31063 AN: 67944

Other (OTH) AF: 0.510 AC: 1077 AN: 2112

Alfa AF: 0.489 Hom.: 80165

Bravo AF: 0.578

Asia WGS AF: 0.480 AC: 1666 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.6
DANN	Benign	0.31
PhyloP100		0.20
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: rs10485358; hg19: chr6-64386060;