9-34737831-C-T

Variant names:

• chr9-34737831-C-T
• rs2492358
• XM_047423102.1:c.133+34793C>T

Variant summary

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

The ENST00000664167.1(ENSG00000230074):​n.86+34793C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.781 in 152,100 control chromosomes in the GnomAD database, including 47,043 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 0.78 (47043 hom., cov: 33)
• Consequence: ENSG00000230074 ENST00000664167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.763
• Publications: 10 publications found

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]

ENSG00000230074 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.925 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000664167.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000230074	ENST00000664167.1		n.86+34793C>T		intron	N/A
	ENSG00000230074	ENST00000837930.1		n.174+34793C>T		intron	N/A
	ENSG00000230074	ENST00000837931.1		n.306+34793C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118729 AN: 151982 Hom.: 47027 Cov.: 33

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.623

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.947

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.785

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

GnomAD4 genome AF: 0.781 AC: 118785 AN: 152100 Hom.: 47043 Cov.: 33 AF XY: 0.782 AC XY: 58174 AN XY: 74352

African (AFR) AF: 0.647 AC: 26811 AN: 41436

American (AMR) AF: 0.818 AC: 12492 AN: 15268

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3472

East Asian (EAS) AF: 0.947 AC: 4913 AN: 5190

South Asian (SAS) AF: 0.781 AC: 3765 AN: 4822

European-Finnish (FIN) AF: 0.825 AC: 8731 AN: 10586

Middle Eastern (MID) AF: 0.704 AC: 207 AN: 294

European-Non Finnish (NFE) AF: 0.839 AC: 57083 AN: 68004

Other (OTH) AF: 0.788 AC: 1667 AN: 2116

Alfa AF: 0.816 Hom.: 35868

Bravo AF: 0.775

Asia WGS AF: 0.843 AC: 2930 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.25
DANN	Benign	0.69
PhyloP100		-0.76

Splicing

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

Other links and lift over

dbSNP: rs2492358; hg19: chr9-34737828;