rs3933326

chr9-120871670-A-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_015651.3(PHF19):c.269-1132T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,006 control chromosomes in the GnomAD database, including 32,705 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 0.65 (32705 hom., cov: 32)
• Consequence: PHF19 NM_015651.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980

Genes affected

PHF19 (HGNC:24566): (PHD finger protein 19) Enables methylated histone binding activity. Involved in positive regulation of histone H3-K27 methylation. Colocalizes with ESC/E(Z) complex. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.764 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF19	NM_015651.3	c.269-1132T>C		intron_variant		ENST00000373896.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF19	ENST00000373896.8	c.269-1132T>C		intron_variant		2	NM_015651.3	P1

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98985 AN: 151888 Hom.: 32666 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.652 AC: 99072 AN: 152006 Hom.: 32705 Cov.: 32 AF XY: 0.655 AC XY: 48667 AN XY: 74284

Gnomad4 AFR AF: 0.568

Gnomad4 AMR AF: 0.775

Gnomad4 ASJ AF: 0.764

Gnomad4 EAS AF: 0.502

Gnomad4 SAS AF: 0.784

Gnomad4 FIN AF: 0.623

Gnomad4 NFE AF: 0.677

Gnomad4 OTH AF: 0.681

Alfa AF: 0.681 Hom.: 46084

Bravo AF: 0.657

Asia WGS AF: 0.646 AC: 2247 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.044
Dann	Benign	0.34

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

Publications

LitVar

Other links and lift over

dbSNP: rs3933326; hg19: chr9-123633948;