rs10814138

Variant names:

• chr9-34723038-C-A
• rs10814138
• XM_047423102.1:c.133+20000C>A

Your query was ambiguous. Multiple possible variants found:

• chr9-34723038-C-A
• chr9-34723038-C-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The XM_047423102.1(PHF24):​c.133+20000C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.25 in 708,848 control chromosomes in the GnomAD database, including 25,119 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 0.21 (4275 hom., cov: 32)
  • Exomes 𝑓: 0.26 (20844 hom.)
• Consequence: PHF24 XM_047423102.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -3.14

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]

ENSG00000288583 (HGNC:):

SPATA31F1 (HGNC:41911): (SPATA31 subfamily F member 1) Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.301 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
PHF24	XM_047423102.1	c.133+20000C>A		intron_variant	Intron 4 of 11		XP_047279058.1
PHF24	XM_047423103.1	c.70+20000C>A		intron_variant	Intron 2 of 9		XP_047279059.1
SPATA31F1	NM_001141917.2	c.*194G>T		downstream_gene_variant		ENST00000378788.4	NP_001135389.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ENSG00000288583	ENST00000664167.1	n.86+20000C>A		intron_variant	Intron 1 of 1
FAM205A	ENST00000378788.4	c.*194G>T		downstream_gene_variant		2	NM_001141917.2	ENSP00000417711.1

Frequencies

GnomAD3 genomes AF: 0.208 AC: 31593 AN: 152030 Hom.: 4277 Cov.: 32

Gnomad AFR AF: 0.0546

Gnomad AMI AF: 0.316

Gnomad AMR AF: 0.205

Gnomad ASJ AF: 0.197

Gnomad EAS AF: 0.0529

Gnomad SAS AF: 0.195

Gnomad FIN AF: 0.267

Gnomad MID AF: 0.212

Gnomad NFE AF: 0.304

Gnomad OTH AF: 0.208

GnomAD4 exome AF: 0.262 AC: 145824 AN: 556700 Hom.: 20844 Cov.: 7 AF XY: 0.259 AC XY: 73903 AN XY: 285050

Gnomad4 AFR exome AF: 0.0509

Gnomad4 AMR exome AF: 0.196

Gnomad4 ASJ exome AF: 0.204

Gnomad4 EAS exome AF: 0.0428

Gnomad4 SAS exome AF: 0.201

Gnomad4 FIN exome AF: 0.283

Gnomad4 NFE exome AF: 0.301

Gnomad4 OTH exome AF: 0.245

GnomAD4 genome AF: 0.208 AC: 31589 AN: 152148 Hom.: 4275 Cov.: 32 AF XY: 0.205 AC XY: 15240 AN XY: 74364

Gnomad4 AFR AF: 0.0544

Gnomad4 AMR AF: 0.205

Gnomad4 ASJ AF: 0.197

Gnomad4 EAS AF: 0.0535

Gnomad4 SAS AF: 0.195

Gnomad4 FIN AF: 0.267

Gnomad4 NFE AF: 0.304

Gnomad4 OTH AF: 0.206

Alfa AF: 0.277 Hom.: 8061

Bravo AF: 0.196

Asia WGS AF: 0.108 AC: 374 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.13
DANN	Benign	0.31

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs10814138; hg19: chr9-34723035;