ENST00000664167.1:n.86+10490A>G

Variant names:

• chr9-34713528-A-G
• rs10972206
• ENST00000664167.1:n.86+10490A>G

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_Strong BS2

The ENST00000664167.1(ENSG00000230074):​n.86+10490A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00792 in 152,090 control chromosomes in the GnomAD database, including 9 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 0.0079 (9 hom., cov: 32)
• Consequence: ENSG00000230074 ENST00000664167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.34
• Publications: 1 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 -8 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BS2: High Homozygotes in GnomAd4 at 9 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+10490A>G		intron_variant	Intron 4 of 11		XP_047279058.1
PHF24	XM_047423103.1	c.70+10490A>G		intron_variant	Intron 2 of 9		XP_047279059.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000230074	ENST00000664167.1	n.86+10490A>G		intron_variant	Intron 1 of 1
ENSG00000230074	ENST00000837930.1	n.174+10490A>G		intron_variant	Intron 2 of 3
ENSG00000230074	ENST00000837931.1	n.306+10490A>G		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.00792 AC: 1203 AN: 151972 Hom.: 9 Cov.: 32

Gnomad AFR AF: 0.00256

Gnomad AMI AF: 0.00987

Gnomad AMR AF: 0.00557

Gnomad ASJ AF: 0.00144

Gnomad EAS AF: 0.000579

Gnomad SAS AF: 0.00436

Gnomad FIN AF: 0.00388

Gnomad MID AF: 0.00316

Gnomad NFE AF: 0.0136

Gnomad OTH AF: 0.00432

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

GnomAD4 genome AF: 0.00792 AC: 1205 AN: 152090 Hom.: 9 Cov.: 32 AF XY: 0.00710 AC XY: 528 AN XY: 74346

African (AFR) AF: 0.00256 AC: 106 AN: 41486

American (AMR) AF: 0.00557 AC: 85 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.00144 AC: 5 AN: 3464

East Asian (EAS) AF: 0.000774 AC: 4 AN: 5170

South Asian (SAS) AF: 0.00457 AC: 22 AN: 4810

European-Finnish (FIN) AF: 0.00388 AC: 41 AN: 10564

Middle Eastern (MID) AF: 0.00340 AC: 1 AN: 294

European-Non Finnish (NFE) AF: 0.0136 AC: 923 AN: 68014

Other (OTH) AF: 0.00428 AC: 9 AN: 2104

Alfa AF: 0.0100 Hom.: 5

Bravo AF: 0.00783

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.054
DANN	Benign	0.18
PhyloP100		-1.3

Splicing

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

Other links and lift over

dbSNP: rs10972206; hg19: chr9-34713525;