rs10758278

Variant names:

• chr9-34825306-G-A
• rs10758278
• XM_047423102.1:c.134-64273G>A

Variant summary

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

The XM_047423102.1(PHF24):​c.134-64273G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.53 in 151,772 control chromosomes in the GnomAD database, including 23,153 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 0.53 (23153 hom., cov: 29)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825

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]

ENSG00000287368 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.639 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.134-64273G>A		intron_variant	Intron 4 of 11		XP_047279058.1
PHF24	XM_047423103.1	c.71-64273G>A		intron_variant	Intron 2 of 9		XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000287368	ENST00000658462.1	n.140+15147G>A		intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes AF: 0.531 AC: 80470 AN: 151656 Hom.: 23146 Cov.: 29

Gnomad AFR AF: 0.311

Gnomad AMI AF: 0.688

Gnomad AMR AF: 0.590

Gnomad ASJ AF: 0.613

Gnomad EAS AF: 0.312

Gnomad SAS AF: 0.465

Gnomad FIN AF: 0.658

Gnomad MID AF: 0.611

Gnomad NFE AF: 0.644

Gnomad OTH AF: 0.575

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

GnomAD4 genome AF: 0.530 AC: 80498 AN: 151772 Hom.: 23153 Cov.: 29 AF XY: 0.529 AC XY: 39209 AN XY: 74178

Gnomad4 AFR AF: 0.310

Gnomad4 AMR AF: 0.591

Gnomad4 ASJ AF: 0.613

Gnomad4 EAS AF: 0.312

Gnomad4 SAS AF: 0.465

Gnomad4 FIN AF: 0.658

Gnomad4 NFE AF: 0.644

Gnomad4 OTH AF: 0.574

Alfa AF: 0.590 Hom.: 3480

Bravo AF: 0.519

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	2.5
DANN	Benign	0.62

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10758278; hg19: chr9-34825303;