rs277606

Positions:

• chr9-34785311-T-C

Variant summary

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

The XM_047423102.1(PHF24):​c.133+82273T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.513 in 152,094 control chromosomes in the GnomAD database, including 22,520 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 0.51 (22520 hom., cov: 32)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.891

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.641 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+82273T>C		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.70+82273T>C		intron_variant			XP_047279059.1
		n.34785311T>C		intergenic_region

Ensembl

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

Frequencies

GnomAD3 genomes AF: 0.514 AC: 78064 AN: 151976 Hom.: 22514 Cov.: 32

Gnomad AFR AF: 0.249

Gnomad AMI AF: 0.568

Gnomad AMR AF: 0.584

Gnomad ASJ AF: 0.573

Gnomad EAS AF: 0.314

Gnomad SAS AF: 0.473

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.604

Gnomad NFE AF: 0.646

Gnomad OTH AF: 0.562

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

GnomAD4 genome AF: 0.513 AC: 78080 AN: 152094 Hom.: 22520 Cov.: 32 AF XY: 0.513 AC XY: 38163 AN XY: 74354

Gnomad4 AFR AF: 0.248

Gnomad4 AMR AF: 0.584

Gnomad4 ASJ AF: 0.573

Gnomad4 EAS AF: 0.314

Gnomad4 SAS AF: 0.473

Gnomad4 FIN AF: 0.677

Gnomad4 NFE AF: 0.646

Gnomad4 OTH AF: 0.560

Alfa AF: 0.624 Hom.: 39657

Bravo AF: 0.498

Asia WGS AF: 0.386 AC: 1346 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	3.9
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs277606; hg19: chr9-34785308;