9-34691559-A-G

Position:

• chr9-34691559-A-G

Variant summary

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

The XM_047423102.1(PHF24):​c.48+10342A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,158 control chromosomes in the GnomAD database, including 3,521 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 0.21 (3521 hom., cov: 32)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.48+10342A>G		intron_variant			XP_047279058.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31843 AN: 152040 Hom.: 3516 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.209 AC: 31846 AN: 152158 Hom.: 3521 Cov.: 32 AF XY: 0.209 AC XY: 15565 AN XY: 74404

Gnomad4 AFR AF: 0.147

Gnomad4 AMR AF: 0.209

Gnomad4 ASJ AF: 0.266

Gnomad4 EAS AF: 0.0634

Gnomad4 SAS AF: 0.252

Gnomad4 FIN AF: 0.228

Gnomad4 NFE AF: 0.249

Gnomad4 OTH AF: 0.200

Alfa AF: 0.238 Hom.: 718

Bravo AF: 0.202

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.56

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2233872; hg19: chr9-34691556;