rs1057530

chr6-63717199-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.*3491C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.536 in 151,856 control chromosomes in the GnomAD database, including 23,172 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 0.54 (23172 hom., cov: 32)
• Consequence: PHF3 NM_001370348.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.295

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=-0.98).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.725 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF3	NM_001370348.2	c.*3491C>T		3_prime_UTR_variant	16/16	ENST00000262043.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF3	ENST00000262043.8	c.*3491C>T		3_prime_UTR_variant	16/16	5	NM_001370348.2	P1
PHF3	ENST00000505138.1	c.363+5837C>T		intron_variant		3

Frequencies

GnomAD3 genomes AF: 0.536 AC: 81266 AN: 151738 Hom.: 23124 Cov.: 32

Gnomad AFR AF: 0.732

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.551

Gnomad ASJ AF: 0.471

Gnomad EAS AF: 0.461

Gnomad SAS AF: 0.560

Gnomad FIN AF: 0.357

Gnomad MID AF: 0.481

Gnomad NFE AF: 0.450

Gnomad OTH AF: 0.500

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

GnomAD4 genome AF: 0.536 AC: 81369 AN: 151856 Hom.: 23172 Cov.: 32 AF XY: 0.535 AC XY: 39681 AN XY: 74224

Gnomad4 AFR AF: 0.732

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.471

Gnomad4 EAS AF: 0.461

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.357

Gnomad4 NFE AF: 0.450

Gnomad4 OTH AF: 0.496

Alfa AF: 0.471 Hom.: 17038

Bravo AF: 0.559

Asia WGS AF: 0.482 AC: 1672 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
Cadd	Benign	0.67
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1057530; hg19: chr6-64427095;