rs1953126

Positions:

• chr9-120878222-T-C

Variant summary

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

The ENST00000616568.5(PHF19):​c.43-3466A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.684 in 152,018 control chromosomes in the GnomAD database, including 35,785 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 0.68 (35785 hom., cov: 32)
• Consequence: PHF19 ENST00000616568.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.202

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 = 0.776 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF19	NM_001286840.1	c.43-3466A>G		intron_variant
PHF19	XM_011518515.3	c.43-3466A>G		intron_variant
PHF19	XM_011518516.3	c.43-3466A>G		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF19	ENST00000616568.5	c.43-3466A>G		intron_variant		1

Frequencies

GnomAD3 genomes AF: 0.684 AC: 103852 AN: 151900 Hom.: 35736 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.696

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.674

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.699

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

GnomAD4 genome AF: 0.684 AC: 103953 AN: 152018 Hom.: 35785 Cov.: 32 AF XY: 0.684 AC XY: 50788 AN XY: 74296

Gnomad4 AFR AF: 0.755

Gnomad4 AMR AF: 0.696

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.674

Gnomad4 SAS AF: 0.797

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.699

Alfa AF: 0.665 Hom.: 52666

Bravo AF: 0.694

Asia WGS AF: 0.741 AC: 2575 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	6.4
DANN	Benign	0.37

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1953126; hg19: chr9-123640500; COSMIC: COSV56490069; COSMIC: COSV56490069;