chr9-120881577-T-C

Variant names:

• chr9-120881577-T-C
• rs10985073
• ENST00000616568.5:c.43-6821A>G

Variant summary

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

The ENST00000616568.5(PHF19):​c.43-6821A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 152,088 control chromosomes in the GnomAD database, including 17,933 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 0.45 (17933 hom., cov: 32)
• Consequence: PHF19 ENST00000616568.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.44
• Publications: 31 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=-0.87).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.655 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000616568.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF19	NM_001286840.1		c.43-6821A>G		intron	N/A	NP_001273769.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF19	ENST00000616568.5	TSL:1	c.43-6821A>G		intron	N/A	ENSP00000483946.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67884 AN: 151970 Hom.: 17921 Cov.: 32

Gnomad AFR AF: 0.142

Gnomad AMI AF: 0.434

Gnomad AMR AF: 0.562

Gnomad ASJ AF: 0.662

Gnomad EAS AF: 0.495

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.542

Gnomad MID AF: 0.652

Gnomad NFE AF: 0.558

Gnomad OTH AF: 0.516

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

GnomAD4 genome AF: 0.446 AC: 67905 AN: 152088 Hom.: 17933 Cov.: 32 AF XY: 0.453 AC XY: 33673 AN XY: 74338

African (AFR) AF: 0.142 AC: 5877 AN: 41510

American (AMR) AF: 0.563 AC: 8596 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.662 AC: 2298 AN: 3470

East Asian (EAS) AF: 0.495 AC: 2564 AN: 5178

South Asian (SAS) AF: 0.674 AC: 3252 AN: 4824

European-Finnish (FIN) AF: 0.542 AC: 5723 AN: 10554

Middle Eastern (MID) AF: 0.643 AC: 189 AN: 294

European-Non Finnish (NFE) AF: 0.558 AC: 37924 AN: 67960

Other (OTH) AF: 0.516 AC: 1088 AN: 2110

Alfa AF: 0.541 Hom.: 35187

Bravo AF: 0.434

Asia WGS AF: 0.553 AC: 1920 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.8
DANN	Benign	0.72
PhyloP100		1.4

Splicing

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

Other links and lift over

dbSNP: rs10985073; hg19: chr9-123643855;