rs1057530

Variant names:

• chr6-63717199-C-T
• rs1057530
• NM_001370348.2:c.*3491C>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.*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
• Publications: 6 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=-0.98).
• 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 rank	MANE	Protein	UniProt
PHF3	NM_001370348.2	c.*3491C>T		3_prime_UTR_variant	Exon 16 of 16	ENST00000262043.8	NP_001357277.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF3	ENST00000262043.8	c.*3491C>T		3_prime_UTR_variant	Exon 16 of 16	5	NM_001370348.2	ENSP00000262043.4
PHF3	ENST00000505138.1	c.361+5837C>T		intron_variant	Intron 3 of 4	3		ENSP00000421417.1

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

African (AFR) AF: 0.732 AC: 30317 AN: 41436

American (AMR) AF: 0.552 AC: 8393 AN: 15214

Ashkenazi Jewish (ASJ) AF: 0.471 AC: 1634 AN: 3470

East Asian (EAS) AF: 0.461 AC: 2376 AN: 5154

South Asian (SAS) AF: 0.561 AC: 2708 AN: 4824

European-Finnish (FIN) AF: 0.357 AC: 3773 AN: 10564

Middle Eastern (MID) AF: 0.486 AC: 143 AN: 294

European-Non Finnish (NFE) AF: 0.450 AC: 30534 AN: 67878

Other (OTH) AF: 0.496 AC: 1047 AN: 2112

Alfa AF: 0.475 Hom.: 20854

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
PhyloP100		-0.29

Splicing

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

Other links and lift over

dbSNP: rs1057530; hg19: chr6-64427095;