9-34710341-G-A

Position:

• chr9-34710341-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+7303G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.242 in 152,008 control chromosomes in the GnomAD database, including 5,343 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 0.24 (5343 hom., cov: 32)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.87

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=-0.81).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.328 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+7303G>A		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.70+7303G>A		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288583	ENST00000664167.1	n.86+7303G>A		intron_variant

Frequencies

GnomAD3 genomes AF: 0.242 AC: 36761 AN: 151890 Hom.: 5343 Cov.: 32

Gnomad AFR AF: 0.0957

Gnomad AMI AF: 0.321

Gnomad AMR AF: 0.255

Gnomad ASJ AF: 0.228

Gnomad EAS AF: 0.0693

Gnomad SAS AF: 0.338

Gnomad FIN AF: 0.262

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.331

Gnomad OTH AF: 0.232

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

GnomAD4 genome AF: 0.242 AC: 36777 AN: 152008 Hom.: 5343 Cov.: 32 AF XY: 0.240 AC XY: 17796 AN XY: 74270

Gnomad4 AFR AF: 0.0956

Gnomad4 AMR AF: 0.255

Gnomad4 ASJ AF: 0.228

Gnomad4 EAS AF: 0.0699

Gnomad4 SAS AF: 0.339

Gnomad4 FIN AF: 0.262

Gnomad4 NFE AF: 0.331

Gnomad4 OTH AF: 0.230

Alfa AF: 0.312 Hom.: 10199

Bravo AF: 0.233

Asia WGS AF: 0.196 AC: 680 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.81
CADD	Benign	11
DANN	Benign	0.57

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs11574914; hg19: chr9-34710338;