rs2812377

Variant names:

• chr9-34710453-A-C
• rs2812377
• ENST00000664167.1:n.86+7415A>C

Your query was ambiguous. Multiple possible variants found:

• chr9-34710453-A-C
• chr9-34710453-A-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+7415A>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 148,846 control chromosomes in the GnomAD database, including 6,762 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 0.29 (6762 hom., cov: 29)
• Consequence: ENSG00000230074 ENST00000664167.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.307
• Publications: 7 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+7415A>C		intron_variant	Intron 4 of 11		XP_047279058.1
PHF24	XM_047423103.1	c.70+7415A>C		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+7415A>C		intron_variant	Intron 1 of 1
ENSG00000230074	ENST00000837930.1	n.174+7415A>C		intron_variant	Intron 2 of 3
ENSG00000230074	ENST00000837931.1	n.306+7415A>C		intron_variant	Intron 2 of 3

Frequencies

GnomAD3 genomes AF: 0.292 AC: 43394 AN: 148748 Hom.: 6763 Cov.: 29

Gnomad AFR AF: 0.183

Gnomad AMI AF: 0.258

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.340

Gnomad EAS AF: 0.313

Gnomad SAS AF: 0.269

Gnomad FIN AF: 0.343

Gnomad MID AF: 0.306

Gnomad NFE AF: 0.334

Gnomad OTH AF: 0.318

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

GnomAD4 genome AF: 0.292 AC: 43396 AN: 148846 Hom.: 6762 Cov.: 29 AF XY: 0.293 AC XY: 21185 AN XY: 72266

African (AFR) AF: 0.183 AC: 7433 AN: 40584

American (AMR) AF: 0.350 AC: 5176 AN: 14768

Ashkenazi Jewish (ASJ) AF: 0.340 AC: 1177 AN: 3460

East Asian (EAS) AF: 0.312 AC: 1525 AN: 4882

South Asian (SAS) AF: 0.268 AC: 1260 AN: 4702

European-Finnish (FIN) AF: 0.343 AC: 3285 AN: 9590

Middle Eastern (MID) AF: 0.304 AC: 87 AN: 286

European-Non Finnish (NFE) AF: 0.334 AC: 22567 AN: 67614

Other (OTH) AF: 0.317 AC: 654 AN: 2062

Alfa AF: 0.319 Hom.: 29699

Bravo AF: 0.289

Asia WGS AF: 0.250 AC: 873 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.3
DANN	Benign	0.85
PhyloP100		-0.31
PromoterAI		-0.020	Neutral

Splicing

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

Other links and lift over

dbSNP: rs2812377; hg19: chr9-34710450; COSMIC: COSV52398698;