9-34713528-A-G

Position:

• chr9-34713528-A-G

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BP4_Strong BS2

The XM_047423102.1(PHF24):​c.133+10490A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00792 in 152,090 control chromosomes in the GnomAD database, including 9 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 0.0079 (9 hom., cov: 32)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34

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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+10490A>G		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.70+10490A>G		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288583	ENST00000664167.1	n.86+10490A>G		intron_variant

Frequencies

GnomAD3 genomes AF: 0.00792 AC: 1203 AN: 151972 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.00557

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.00388

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.00432

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

GnomAD4 genome AF: 0.00792 AC: 1205 AN: 152090 Hom.: 9 Cov.: 32 AF XY: 0.00710 AC XY: 528 AN XY: 74346

Gnomad4 AFR AF: 0.00256

Gnomad4 AMR AF: 0.00557

Gnomad4 ASJ AF: 0.00144

Gnomad4 EAS AF: 0.000774

Gnomad4 SAS AF: 0.00457

Gnomad4 FIN AF: 0.00388

Gnomad4 NFE AF: 0.0136

Gnomad4 OTH AF: 0.00428

Alfa AF: 0.00995 Hom.: 1

Bravo AF: 0.00783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.18

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10972206; hg19: chr9-34713525;