9-120880073-C-T

Position:

• chr9-120880073-C-T

Variant summary

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

The NM_001286840.1(PHF19):​c.43-5317G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.686 in 152,036 control chromosomes in the GnomAD database, including 36,063 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 0.69 (36063 hom., cov: 32)
• Consequence: PHF19 NM_001286840.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841

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 = 0.777 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF19	NM_001286840.1	c.43-5317G>A		intron_variant			NP_001273769.1
PHF19	XM_017014612.3	c.-15-5317G>A		intron_variant			XP_016870101.1
PHF19	XM_047423210.1	c.43-5317G>A		intron_variant			XP_047279166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
PHF19	ENST00000616568.5	c.43-5317G>A		intron_variant		1		ENSP00000483946.1

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104234 AN: 151918 Hom.: 36014 Cov.: 32

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.704

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.577

Gnomad MID AF: 0.807

Gnomad NFE AF: 0.645

Gnomad OTH AF: 0.707

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

GnomAD4 genome AF: 0.686 AC: 104334 AN: 152036 Hom.: 36063 Cov.: 32 AF XY: 0.686 AC XY: 50980 AN XY: 74308

Gnomad4 AFR AF: 0.756

Gnomad4 AMR AF: 0.704

Gnomad4 ASJ AF: 0.744

Gnomad4 EAS AF: 0.720

Gnomad4 SAS AF: 0.798

Gnomad4 FIN AF: 0.577

Gnomad4 NFE AF: 0.645

Gnomad4 OTH AF: 0.707

Alfa AF: 0.671 Hom.: 31820

Bravo AF: 0.697

Asia WGS AF: 0.767 AC: 2664 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	0.89
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs1609810; hg19: chr9-123642351;