chr6-63716998-A-G

Variant names:

• chr6-63716998-A-G
• rs4710437
• NM_001370348.2:c.*3290A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001370348.2(PHF3):​c.*3290A>G variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.539 in 151,802 control chromosomes in the GnomAD database, including 23,408 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 (23408 hom., cov: 32)
• Consequence: PHF3 NM_001370348.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• 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=-0.94).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.727 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF3	NM_001370348.2	c.*3290A>G		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.*3290A>G		3_prime_UTR_variant	Exon 16 of 16	5	NM_001370348.2	ENSP00000262043.4
PHF3	ENST00000505138.1	c.361+5636A>G		intron_variant	Intron 3 of 4	3		ENSP00000421417.1

Frequencies

GnomAD3 genomes AF: 0.539 AC: 81752 AN: 151684 Hom.: 23360 Cov.: 32

Gnomad AFR AF: 0.734

Gnomad AMI AF: 0.492

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.474

Gnomad EAS AF: 0.459

Gnomad SAS AF: 0.564

Gnomad FIN AF: 0.358

Gnomad MID AF: 0.487

Gnomad NFE AF: 0.455

Gnomad OTH AF: 0.503

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

GnomAD4 genome AF: 0.539 AC: 81855 AN: 151802 Hom.: 23408 Cov.: 32 AF XY: 0.538 AC XY: 39907 AN XY: 74208

African (AFR) AF: 0.734 AC: 30384 AN: 41414

American (AMR) AF: 0.557 AC: 8466 AN: 15212

Ashkenazi Jewish (ASJ) AF: 0.474 AC: 1640 AN: 3462

East Asian (EAS) AF: 0.458 AC: 2362 AN: 5152

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

European-Finnish (FIN) AF: 0.358 AC: 3779 AN: 10558

Middle Eastern (MID) AF: 0.493 AC: 144 AN: 292

European-Non Finnish (NFE) AF: 0.455 AC: 30855 AN: 67868

Other (OTH) AF: 0.499 AC: 1054 AN: 2112

Alfa AF: 0.338 Hom.: 856

Bravo AF: 0.562

Asia WGS AF: 0.483 AC: 1677 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.20
DANN	Benign	0.44
PhyloP100		-1.5

Splicing

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

Other links and lift over

dbSNP: rs4710437; hg19: chr6-64426894;