Variant 9-34710263-G-A details in Genebe, Genetics Data Aggregator

Variant summary

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

The XM_047423102.1(PHF24):c.133+7225G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.683 in 592,598 control chromosomes in the GnomAD database, including 140,475 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 0.67 ( 34177 hom., cov: 31)

Exomes 𝑓: 0.69 ( 106298 hom. )

Consequence

PHF24
XM_047423102.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.223

Variant links:

Genes affected

PHF24 (HGNC:29180): (PHD finger protein 24) Predicted to enable metal ion binding activity. Predicted to act upstream of or within several processes, including detection of mechanical stimulus involved in sensory perception of pain; gamma-aminobutyric acid signaling pathway; and regulation of GABAergic synaptic transmission. [provided by Alliance of Genome Resources, Apr 2022]

PHF24 links:

ENSG00000288583 (HGNC:):

ENSG00000288583 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=-0.99).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.908 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1 linkuse as main transcript	c.133+7225G>A		intron_variant			XP_047279058.1
PHF24	XM_047423103.1 linkuse as main transcript	c.70+7225G>A		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288583	ENST00000664167.1 linkuse as main transcript	n.86+7225G>A		intron_variant

Frequencies

GnomAD3 genomes

AF:

0.666

AC:

101177

AN:

151924

Hom.:

34168

Cov.:

show subpopulations

Gnomad AFR

AF:

0.589

Gnomad AMI

AF:

0.680

Gnomad AMR

AF:

0.708

Gnomad ASJ

AF:

0.728

Gnomad EAS

AF:

0.931

Gnomad SAS

AF:

0.663

Gnomad FIN

AF:

0.739

Gnomad MID

AF:

0.702

Gnomad NFE

AF:

0.667

Gnomad OTH

AF:

0.697

GnomAD4 exome

AF:

0.689

AC:

303746

AN:

440552

Hom.:

106298

AF XY:

0.689

AC XY:

159386

AN XY:

231340

show subpopulations

Gnomad4 AFR exome

AF:

0.587

Gnomad4 AMR exome

AF:

0.715

Gnomad4 ASJ exome

AF:

0.724

Gnomad4 EAS exome

AF:

0.948

Gnomad4 SAS exome

AF:

0.655

Gnomad4 FIN exome

AF:

0.722

Gnomad4 NFE exome

AF:

0.663

Gnomad4 OTH exome

AF:

0.688

GnomAD4 genome

AF:

0.666

AC:

101223

AN:

152046

Hom.:

34177

Cov.:

AF XY:

0.671

AC XY:

49885

AN XY:

74308

show subpopulations

Gnomad4 AFR

AF:

0.589

Gnomad4 AMR

AF:

0.708

Gnomad4 ASJ

AF:

0.728

Gnomad4 EAS

AF:

0.930

Gnomad4 SAS

AF:

0.661

Gnomad4 FIN

AF:

0.739

Gnomad4 NFE

AF:

0.667

Gnomad4 OTH

AF:

0.700

Alfa

AF:

0.670

Hom.:

34156

Bravo

AF:

0.661

Asia WGS

AF:

0.778

AC:

2709

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.99

CADD

Benign

0.96

DANN

Benign

0.22

Splicing

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