9-120895224-G-C

Variant names:

• chr9-120895224-G-C
• rs1468671
• XM_017014612.3:c.-16+6666C>G

Variant summary

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

The XM_017014612.3(PHF19):​c.-16+6666C>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.687 in 151,994 control chromosomes in the GnomAD database, including 36,128 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 (36128 hom., cov: 30)
• Consequence: PHF19 XM_017014612.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.282
• Publications: 11 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 = 0.796 is higher than 0.05.

Variant Effect in Transcripts

 

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.687 AC: 104286 AN: 151876 Hom.: 36082 Cov.: 30

Gnomad AFR AF: 0.756

Gnomad AMI AF: 0.488

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.817

Gnomad FIN AF: 0.576

Gnomad MID AF: 0.804

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: 0.687 AC: 104382 AN: 151994 Hom.: 36128 Cov.: 30 AF XY: 0.687 AC XY: 51035 AN XY: 74298

African (AFR) AF: 0.756 AC: 31335 AN: 41442

American (AMR) AF: 0.703 AC: 10748 AN: 15282

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

East Asian (EAS) AF: 0.719 AC: 3713 AN: 5164

South Asian (SAS) AF: 0.817 AC: 3947 AN: 4830

European-Finnish (FIN) AF: 0.576 AC: 6079 AN: 10554

Middle Eastern (MID) AF: 0.799 AC: 235 AN: 294

European-Non Finnish (NFE) AF: 0.645 AC: 43807 AN: 67934

Other (OTH) AF: 0.706 AC: 1492 AN: 2114

Alfa AF: 0.668 Hom.: 4238

Bravo AF: 0.697

Asia WGS AF: 0.773 AC: 2687 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	1.8
DANN	Benign	0.51
PhyloP100		-0.28
PromoterAI		0.0010	Neutral

Splicing

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

Other links and lift over

dbSNP: rs1468671; hg19: chr9-123657502;