rs10758278

Variant names:

• chr9-34825306-G-A
• rs10758278
• ENST00000658462.1:n.140+15147G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000658462.1(ENSG00000230074):​n.140+15147G>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: ENSG00000230074 ENST00000658462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.825
• Publications: 4 publications found

Genes affected

ENSG00000230074 (HGNC:):

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

Our verdict: Benign. The variant received -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
ENSG00000230074	ENST00000658462.1	n.140+15147G>A		intron_variant	Intron 1 of 2
ENSG00000230074	ENST00000837930.1	n.175-64273G>A		intron_variant	Intron 2 of 3
ENSG00000230074	ENST00000837931.1	n.307-64273G>A		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.310 AC: 12846 AN: 41394

American (AMR) AF: 0.591 AC: 9009 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.613 AC: 2125 AN: 3468

East Asian (EAS) AF: 0.312 AC: 1606 AN: 5148

South Asian (SAS) AF: 0.465 AC: 2233 AN: 4798

European-Finnish (FIN) AF: 0.658 AC: 6928 AN: 10526

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.644 AC: 43736 AN: 67880

Other (OTH) AF: 0.574 AC: 1211 AN: 2110

Alfa AF: 0.580 Hom.: 3533

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
PhyloP100		-0.82

Splicing

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

Other links and lift over

dbSNP: rs10758278; hg19: chr9-34825303;