Genetic Variant PHF19:c.*1993T>C (chr9-120855951-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_015651.3(PHF19):c.*1993T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.736 in 152,572 control chromosomes in the GnomAD database, including 41,560 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 0.74 ( 41453 hom., cov: 31)

Exomes 𝑓: 0.67 ( 107 hom. )

Consequence

PHF19
NM_015651.3 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.517

Variant links:

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]

PHF19 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.9).

BA1

GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.811 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF19	NM_015651.3 link	c.*1993T>C		3_prime_UTR_variant	Exon 15 of 15	ENST00000373896.8	NP_056466.1	Q5T6S3-1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	MANE	Protein	UniProt
PHF19	ENST00000373896 link	c.*1993T>C	3_prime_UTR_variant	Exon 15 of 15	2	NM_015651.3	ENSP00000363003.3	Q5T6S3-1
PHF19	ENST00000616568 link	c.*1993T>C	3_prime_UTR_variant	Exon 15 of 15	1		ENSP00000483946.1	A0A087X169
PHF19	ENST00000419155 link	c.*1993T>C	3_prime_UTR_variant	Exon 10 of 10	2		ENSP00000407433.1	F5H8K3

Frequencies

GnomAD3 genomes

AF:

0.736

AC:

111904

AN:

151974

Hom.:

41407

Cov.:

show subpopulations

Gnomad AFR

AF:

0.746

Gnomad AMI

AF:

0.692

Gnomad AMR

AF:

0.822

Gnomad ASJ

AF:

0.783

Gnomad EAS

AF:

0.566

Gnomad SAS

AF:

0.796

Gnomad FIN

AF:

0.687

Gnomad MID

AF:

0.803

Gnomad NFE

AF:

0.725

Gnomad OTH

AF:

0.758

GnomAD4 exome

AF:

0.669

AC:

321

AN:

480

Hom.:

107

Cov.:

AF XY:

0.694

AC XY:

204

AN XY:

294

show subpopulations

Gnomad4 FIN exome

AF:

0.658

Gnomad4 NFE exome

AF:

0.738

Gnomad4 OTH exome

AF:

0.833

GnomAD4 genome

AF:

0.736

AC:

112000

AN:

152092

Hom.:

41453

Cov.:

AF XY:

0.738

AC XY:

54851

AN XY:

74320

show subpopulations

Gnomad4 AFR

AF:

0.746

Gnomad4 AMR

AF:

0.823

Gnomad4 ASJ

AF:

0.783

Gnomad4 EAS

AF:

0.565

Gnomad4 SAS

AF:

0.797

Gnomad4 FIN

AF:

0.687

Gnomad4 NFE

AF:

0.725

Gnomad4 OTH

AF:

0.758

Alfa

AF:

0.737

Hom.:

38344

Bravo

AF:

0.746

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.90

CADD

Benign

0.28

DANN

Benign

0.42

RBP_binding_hub_radar

0.0

RBP_regulation_power_radar

1.1

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

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over