9-34868380-C-T

Variant names:

• chr9-34868380-C-T
• rs13290746
• ENST00000658462.1:n.141-21199C>T

Variant summary

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

The ENST00000658462.1(ENSG00000230074):​n.141-21199C>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: ENSG00000230074 ENST00000658462.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0330
• Publications: 3 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=-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 rank	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.134-21199C>T		intron_variant	Intron 4 of 11		XP_047279058.1
PHF24	XM_047423103.1	c.71-21199C>T		intron_variant	Intron 2 of 9		XP_047279059.1
PHF24	XM_017014553.3	c.-65-21199C>T		intron_variant	Intron 2 of 9		XP_016870042.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230074	ENST00000658462.1	n.141-21199C>T		intron_variant	Intron 1 of 2
ENSG00000230074	ENST00000837930.1	n.175-21199C>T		intron_variant	Intron 2 of 3
ENSG00000230074	ENST00000837931.1	n.307-21199C>T		intron_variant	Intron 2 of 3

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

African (AFR) AF: 0.675 AC: 28012 AN: 41490

American (AMR) AF: 0.756 AC: 11547 AN: 15278

Ashkenazi Jewish (ASJ) AF: 0.781 AC: 2710 AN: 3470

East Asian (EAS) AF: 0.871 AC: 4507 AN: 5176

South Asian (SAS) AF: 0.689 AC: 3325 AN: 4826

European-Finnish (FIN) AF: 0.798 AC: 8462 AN: 10600

Middle Eastern (MID) AF: 0.823 AC: 242 AN: 294

European-Non Finnish (NFE) AF: 0.774 AC: 52654 AN: 68012

Other (OTH) AF: 0.779 AC: 1647 AN: 2114

Alfa AF: 0.732 Hom.: 4360

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
PhyloP100		0.033

Splicing

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

Other links and lift over

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