9-120880073-C-T

Variant names:

• chr9-120880073-C-T
• rs1609810
• ENST00000616568.5:c.43-5317G>A

Variant summary

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

The ENST00000616568.5(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 ENST00000616568.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.841
• Publications: 17 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
PHF19	NM_001286840.1	c.43-5317G>A		intron_variant	Intron 1 of 14		NP_001273769.1
PHF19	XM_017014612.3	c.-15-5317G>A		intron_variant	Intron 1 of 14		XP_016870101.1
PHF19	XM_047423210.1	c.43-5317G>A		intron_variant	Intron 1 of 13		XP_047279166.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
PHF19	ENST00000616568.5	c.43-5317G>A		intron_variant	Intron 1 of 14	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

African (AFR) AF: 0.756 AC: 31351 AN: 41474

American (AMR) AF: 0.704 AC: 10757 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2581 AN: 3468

East Asian (EAS) AF: 0.720 AC: 3724 AN: 5174

South Asian (SAS) AF: 0.798 AC: 3846 AN: 4822

European-Finnish (FIN) AF: 0.577 AC: 6082 AN: 10544

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43821 AN: 67966

Other (OTH) AF: 0.707 AC: 1491 AN: 2110

Alfa AF: 0.675 Hom.: 42662

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
PhyloP100		-0.84

Splicing

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

Other links and lift over

dbSNP: rs1609810; hg19: chr9-123642351;