Variant rs10985070 details in Genebe, Genetics Data Aggregator

Variant summary

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

The NM_015651.3(PHF19):c.268+136G>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 631,026 control chromosomes in the GnomAD database, including 98,079 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 0.48 ( 19107 hom., cov: 33)

Exomes 𝑓: 0.57 ( 78972 hom. )

Consequence

PHF19
NM_015651.3 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.163

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=-0.75).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.653 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
PHF19	NM_015651.3 linkuse as main transcript	c.268+136G>T		intron_variant		ENST00000373896.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
PHF19	ENST00000373896.8 linkuse as main transcript	c.268+136G>T		intron_variant		2	NM_015651.3	P1	Q5T6S3-1

Frequencies

GnomAD3 genomes

AF:

0.481

AC:

73032

AN:

151944

Hom.:

19093

Cov.:

show subpopulations

Gnomad AFR

AF:

0.252

Gnomad AMI

AF:

0.455

Gnomad AMR

AF:

0.577

Gnomad ASJ

AF:

0.661

Gnomad EAS

AF:

0.496

Gnomad SAS

AF:

0.670

Gnomad FIN

AF:

0.540

Gnomad MID

AF:

0.668

Gnomad NFE

AF:

0.563

Gnomad OTH

AF:

0.539

GnomAD4 exome

AF:

0.567

AC:

271644

AN:

478964

Hom.:

78972

AF XY:

0.577

AC XY:

146923

AN XY:

254798

show subpopulations

Gnomad4 AFR exome

AF:

0.251

Gnomad4 AMR exome

AF:

0.597

Gnomad4 ASJ exome

AF:

0.645

Gnomad4 EAS exome

AF:

0.476

Gnomad4 SAS exome

AF:

0.684

Gnomad4 FIN exome

AF:

0.524

Gnomad4 NFE exome

AF:

0.574

Gnomad4 OTH exome

AF:

0.559

GnomAD4 genome

AF:

0.481

AC:

73073

AN:

152062

Hom.:

19107

Cov.:

AF XY:

0.487

AC XY:

36189

AN XY:

74310

show subpopulations

Gnomad4 AFR

AF:

0.252

Gnomad4 AMR

AF:

0.578

Gnomad4 ASJ

AF:

0.661

Gnomad4 EAS

AF:

0.497

Gnomad4 SAS

AF:

0.672

Gnomad4 FIN

AF:

0.540

Gnomad4 NFE

AF:

0.563

Gnomad4 OTH

AF:

0.538

Alfa

AF:

0.527

Hom.:

6746

Bravo

AF:

0.472

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.75

CADD

Benign

6.9

DANN

Benign

0.60

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