rs3933326

Variant names:

• chr9-120871670-A-G
• rs3933326
• NM_015651.3:c.269-1132T>C

Variant summary

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

The NM_015651.3(PHF19):​c.269-1132T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.652 in 152,006 control chromosomes in the GnomAD database, including 32,705 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 0.65 (32705 hom., cov: 32)
• Consequence: PHF19 NM_015651.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.980
• 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 = 0.764 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_015651.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF19	NM_015651.3	MANE Select	c.269-1132T>C		intron	N/A	NP_056466.1	Q5T6S3-1
	PHF19	NM_001286840.1		c.326-1132T>C		intron	N/A	NP_001273769.1	A0A087X169
	PHF19	NM_001009936.3		c.269-1132T>C		intron	N/A	NP_001009936.1	Q5T6S3-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	PHF19	ENST00000373896.8	TSL:2 MANE Select	c.269-1132T>C		intron	N/A	ENSP00000363003.3	Q5T6S3-1
	PHF19	ENST00000616568.5	TSL:1	c.326-1132T>C		intron	N/A	ENSP00000483946.1	A0A087X169
	PHF19	ENST00000312189.10	TSL:1	c.269-1132T>C		intron	N/A	ENSP00000310372.6	Q5T6S3-2

Frequencies

GnomAD3 genomes AF: 0.652 AC: 98985 AN: 151888 Hom.: 32666 Cov.: 32

Gnomad AFR AF: 0.568

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.775

Gnomad ASJ AF: 0.764

Gnomad EAS AF: 0.502

Gnomad SAS AF: 0.783

Gnomad FIN AF: 0.623

Gnomad MID AF: 0.750

Gnomad NFE AF: 0.677

Gnomad OTH AF: 0.682

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

GnomAD4 genome AF: 0.652 AC: 99072 AN: 152006 Hom.: 32705 Cov.: 32 AF XY: 0.655 AC XY: 48667 AN XY: 74284

African (AFR) AF: 0.568 AC: 23533 AN: 41434

American (AMR) AF: 0.775 AC: 11860 AN: 15298

Ashkenazi Jewish (ASJ) AF: 0.764 AC: 2649 AN: 3468

East Asian (EAS) AF: 0.502 AC: 2596 AN: 5176

South Asian (SAS) AF: 0.784 AC: 3785 AN: 4826

European-Finnish (FIN) AF: 0.623 AC: 6560 AN: 10524

Middle Eastern (MID) AF: 0.745 AC: 219 AN: 294

European-Non Finnish (NFE) AF: 0.677 AC: 45992 AN: 67968

Other (OTH) AF: 0.681 AC: 1439 AN: 2112

Alfa AF: 0.671 Hom.: 111443

Bravo AF: 0.657

Asia WGS AF: 0.646 AC: 2247 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	0.044
DANN	Benign	0.34
PhyloP100		-0.98
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs3933326; hg19: chr9-123633948;