rs951005

Variant names:

• chr9-34743684-G-A
• rs951005
• XM_047423102.1:c.133+40646G>A

Your query was ambiguous. Multiple possible variants found:

• chr9-34743684-G-A
• chr9-34743684-G-C
• chr9-34743684-G-T

Variant summary

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

The ENST00000664167.1(ENSG00000230074):​n.87-30355G>A 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 152,128 control chromosomes in the GnomAD database, including 47,046 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 (47046 hom., cov: 32)
• Consequence: ENSG00000230074 ENST00000664167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.724
• Publications: 51 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=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.924 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.87-30355G>A		intron	N/A
	ENSG00000230074	ENST00000837930.1		n.174+40646G>A		intron	N/A
	ENSG00000230074	ENST00000837931.1		n.306+40646G>A		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.781 AC: 118749 AN: 152010 Hom.: 47030 Cov.: 32

Gnomad AFR AF: 0.648

Gnomad AMI AF: 0.626

Gnomad AMR AF: 0.818

Gnomad ASJ AF: 0.734

Gnomad EAS AF: 0.946

Gnomad SAS AF: 0.780

Gnomad FIN AF: 0.825

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.839

Gnomad OTH AF: 0.784

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

GnomAD4 genome AF: 0.781 AC: 118805 AN: 152128 Hom.: 47046 Cov.: 32 AF XY: 0.782 AC XY: 58182 AN XY: 74358

African (AFR) AF: 0.647 AC: 26841 AN: 41474

American (AMR) AF: 0.818 AC: 12507 AN: 15294

Ashkenazi Jewish (ASJ) AF: 0.734 AC: 2548 AN: 3470

East Asian (EAS) AF: 0.946 AC: 4904 AN: 5182

South Asian (SAS) AF: 0.781 AC: 3750 AN: 4802

European-Finnish (FIN) AF: 0.825 AC: 8728 AN: 10582

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

European-Non Finnish (NFE) AF: 0.839 AC: 57089 AN: 68010

Other (OTH) AF: 0.787 AC: 1663 AN: 2112

Alfa AF: 0.824 Hom.: 176569

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	-0.95
CADD	Benign	0.22
DANN	Benign	0.32
PhyloP100		-0.72

Splicing

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

Other links and lift over

dbSNP: rs951005; hg19: chr9-34743681;