ENST00000616568.5:c.42+1737A>G

Variant names:

• chr9-120893051-T-C
• rs6478486
• ENST00000616568.5:c.42+1737A>G

Variant summary

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

The ENST00000616568.5(PHF19):​c.42+1737A>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 152,098 control chromosomes in the GnomAD database, including 36,142 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 (36142 hom., cov: 32)
• Consequence: PHF19 ENST00000616568.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.606
• 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=-0.84).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.797 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF19	NM_001286840.1	c.42+1737A>G		intron_variant	Intron 1 of 14		NP_001273769.1
PHF19	XM_017014612.3	c.-16+8839A>G		intron_variant	Intron 1 of 14		XP_016870101.1
PHF19	XM_047423210.1	c.42+1737A>G		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.42+1737A>G		intron_variant	Intron 1 of 14	1		ENSP00000483946.1

Frequencies

GnomAD3 genomes AF: 0.686 AC: 104328 AN: 151980 Hom.: 36095 Cov.: 32

Gnomad AFR AF: 0.755

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.703

Gnomad ASJ AF: 0.744

Gnomad EAS AF: 0.720

Gnomad SAS AF: 0.818

Gnomad FIN AF: 0.577

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: 104426 AN: 152098 Hom.: 36142 Cov.: 32 AF XY: 0.687 AC XY: 51047 AN XY: 74338

African (AFR) AF: 0.756 AC: 31352 AN: 41488

American (AMR) AF: 0.703 AC: 10744 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.744 AC: 2583 AN: 3470

East Asian (EAS) AF: 0.720 AC: 3718 AN: 5162

South Asian (SAS) AF: 0.818 AC: 3938 AN: 4812

European-Finnish (FIN) AF: 0.577 AC: 6103 AN: 10584

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

European-Non Finnish (NFE) AF: 0.645 AC: 43820 AN: 67982

Other (OTH) AF: 0.707 AC: 1492 AN: 2110

Alfa AF: 0.675 Hom.: 43582

Bravo AF: 0.697

Asia WGS AF: 0.774 AC: 2689 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	3.4
DANN	Benign	0.52
PhyloP100		-0.61

Splicing

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

Other links and lift over

dbSNP: rs6478486; hg19: chr9-123655329;