9-34868380-C-T

Position:

• chr9-34868380-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.134-21199C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.747 in 152,170 control chromosomes in the GnomAD database, including 42,725 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 0.75 (42725 hom., cov: 33)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330

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=-1.0).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.85 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.134-21199C>T		intron_variant			XP_047279058.1
PHF24	XM_047423103.1	c.71-21199C>T		intron_variant			XP_047279059.1
PHF24	XM_017014553.3	c.-65-21199C>T		intron_variant			XP_016870042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
ENSG00000287368	ENST00000658462.1	n.141-21199C>T		intron_variant

Frequencies

GnomAD3 genomes AF: 0.747 AC: 113578 AN: 152052 Hom.: 42699 Cov.: 33

Gnomad AFR AF: 0.675

Gnomad AMI AF: 0.605

Gnomad AMR AF: 0.756

Gnomad ASJ AF: 0.781

Gnomad EAS AF: 0.871

Gnomad SAS AF: 0.690

Gnomad FIN AF: 0.798

Gnomad MID AF: 0.832

Gnomad NFE AF: 0.774

Gnomad OTH AF: 0.775

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

GnomAD4 genome AF: 0.747 AC: 113657 AN: 152170 Hom.: 42725 Cov.: 33 AF XY: 0.747 AC XY: 55555 AN XY: 74392

Gnomad4 AFR AF: 0.675

Gnomad4 AMR AF: 0.756

Gnomad4 ASJ AF: 0.781

Gnomad4 EAS AF: 0.871

Gnomad4 SAS AF: 0.689

Gnomad4 FIN AF: 0.798

Gnomad4 NFE AF: 0.774

Gnomad4 OTH AF: 0.779

Alfa AF: 0.735 Hom.: 4175

Bravo AF: 0.747

Asia WGS AF: 0.785 AC: 2732 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	5.3
DANN	Benign	0.32

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs13290746; hg19: chr9-34868377; COSMIC: COSV60353226;