chr9-34743684-G-A

Position:

• chr9-34743684-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047423102.1(PHF24):​c.133+40646G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,128 control chromosomes in the GnomAD database, including 47,046 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 0.78 (47046 hom., cov: 32)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724

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]

ENSG00000288583 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+40646G>A		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.70+40646G>A		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288583	ENST00000664167.1	n.87-30355G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118749 AN: 152010 Hom.: 47030 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.781 AC: 118805 AN: 152128 Hom.: 47046 Cov.: 32 AF XY: 0.782 AC XY: 58182 AN XY: 74358

Gnomad4 AFR AF: 0.647

Gnomad4 AMR AF: 0.818

Gnomad4 ASJ AF: 0.734

Gnomad4 EAS AF: 0.946

Gnomad4 SAS AF: 0.781

Gnomad4 FIN AF: 0.825

Gnomad4 NFE AF: 0.839

Gnomad4 OTH AF: 0.787

Alfa AF: 0.832 Hom.: 75905

Bravo AF: 0.775

Asia WGS AF: 0.843 AC: 2930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	0.22
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs951005; hg19: chr9-34743681;