9-34768696-C-T

Position:

• chr9-34768696-C-T

Variant summary

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

The XM_047423102.1(PHF24):​c.133+65658C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.173 in 152,138 control chromosomes in the GnomAD database, including 3,064 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 0.17 (3064 hom., cov: 32)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.54

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=-0.98).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.255 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+65658C>T		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.70+65658C>T		intron_variant			XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000288583	ENST00000664167.1	n.87-5343C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.174 AC: 26398 AN: 152018 Hom.: 3065 Cov.: 32

Gnomad AFR AF: 0.0453

Gnomad AMI AF: 0.229

Gnomad AMR AF: 0.193

Gnomad ASJ AF: 0.274

Gnomad EAS AF: 0.00945

Gnomad SAS AF: 0.0432

Gnomad FIN AF: 0.202

Gnomad MID AF: 0.226

Gnomad NFE AF: 0.258

Gnomad OTH AF: 0.209

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

GnomAD4 genome AF: 0.173 AC: 26388 AN: 152138 Hom.: 3064 Cov.: 32 AF XY: 0.167 AC XY: 12447 AN XY: 74372

Gnomad4 AFR AF: 0.0452

Gnomad4 AMR AF: 0.192

Gnomad4 ASJ AF: 0.274

Gnomad4 EAS AF: 0.00908

Gnomad4 SAS AF: 0.0435

Gnomad4 FIN AF: 0.202

Gnomad4 NFE AF: 0.258

Gnomad4 OTH AF: 0.206

Alfa AF: 0.238 Hom.: 6175

Bravo AF: 0.169

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.28
DANN	Benign	0.47

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13293020; hg19: chr9-34768693; COSMIC: COSV60353204;