rs2233872

Variant names:

• chr9-34691559-A-G
• rs2233872
• ENST00000837931.1:n.222-11395A>G

Variant summary

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

The ENST00000837931.1(ENSG00000230074):​n.222-11395A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.209 in 152,158 control chromosomes in the GnomAD database, including 3,521 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 0.21 (3521 hom., cov: 32)
• Consequence: ENSG00000230074 ENST00000837931.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.382
• Publications: 5 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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.246 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.48+10342A>G		intron_variant	Intron 3 of 11		XP_047279058.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230074	ENST00000837931.1	n.222-11395A>G		intron_variant	Intron 1 of 3
ENSG00000230074	ENST00000837933.1	n.163-11395A>G		intron_variant	Intron 1 of 2
ENSG00000230074	ENST00000837934.1	n.473+10342A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.209 AC: 31843 AN: 152040 Hom.: 3516 Cov.: 32

Gnomad AFR AF: 0.147

Gnomad AMI AF: 0.273

Gnomad AMR AF: 0.210

Gnomad ASJ AF: 0.266

Gnomad EAS AF: 0.0632

Gnomad SAS AF: 0.251

Gnomad FIN AF: 0.228

Gnomad MID AF: 0.187

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.201

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

GnomAD4 genome AF: 0.209 AC: 31846 AN: 152158 Hom.: 3521 Cov.: 32 AF XY: 0.209 AC XY: 15565 AN XY: 74404

African (AFR) AF: 0.147 AC: 6088 AN: 41520

American (AMR) AF: 0.209 AC: 3202 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.266 AC: 922 AN: 3470

East Asian (EAS) AF: 0.0634 AC: 328 AN: 5176

South Asian (SAS) AF: 0.252 AC: 1216 AN: 4828

European-Finnish (FIN) AF: 0.228 AC: 2411 AN: 10576

Middle Eastern (MID) AF: 0.187 AC: 55 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16952 AN: 67982

Other (OTH) AF: 0.200 AC: 423 AN: 2112

Alfa AF: 0.226 Hom.: 1363

Bravo AF: 0.202

Asia WGS AF: 0.145 AC: 504 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.15
DANN	Benign	0.56
PhyloP100		-0.38
PromoterAI		0.042	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2233872; hg19: chr9-34691556;