9-34890142-A-G

Variant names:

• chr9-34890142-A-G
• rs10123308
• NM_001309427.2:c.359-510T>C

Variant summary

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

The NM_001309427.2(SPATA31F3):​c.359-510T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.473 in 152,000 control chromosomes in the GnomAD database, including 17,991 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 0.47 (17991 hom., cov: 31)
• Consequence: SPATA31F3 NM_001309427.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.98
• Publications: 4 publications found

Genes affected

SPATA31F3 (HGNC:42673): (SPATA31 subfamily F member 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.88).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.557 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001309427.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31F3	NM_001309427.2	MANE Select	c.359-510T>C		intron	N/A	NP_001296356.1
	SPATA31F3	NM_001309426.2		c.746-507T>C		intron	N/A	NP_001296355.1
	SPATA31F3	NM_001375894.1		c.359-507T>C		intron	N/A	NP_001362823.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA31F3	ENST00000340783.11	TSL:4 MANE Select	c.359-510T>C		intron	N/A	ENSP00000489571.1
	SPATA31F3	ENST00000603640.6	TSL:5	c.746-507T>C		intron	N/A	ENSP00000489585.1
	SPATA31F3	ENST00000603592.1	TSL:3	c.355-507T>C		intron	N/A	ENSP00000489523.1

Frequencies

GnomAD3 genomes AF: 0.474 AC: 71919 AN: 151882 Hom.: 17990 Cov.: 31

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.413

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.508

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.316

Gnomad FIN AF: 0.549

Gnomad MID AF: 0.509

Gnomad NFE AF: 0.562

Gnomad OTH AF: 0.512

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

GnomAD4 genome AF: 0.473 AC: 71943 AN: 152000 Hom.: 17991 Cov.: 31 AF XY: 0.468 AC XY: 34776 AN XY: 74292

African (AFR) AF: 0.318 AC: 13171 AN: 41458

American (AMR) AF: 0.530 AC: 8088 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.508 AC: 1762 AN: 3470

East Asian (EAS) AF: 0.352 AC: 1815 AN: 5156

South Asian (SAS) AF: 0.316 AC: 1523 AN: 4824

European-Finnish (FIN) AF: 0.549 AC: 5803 AN: 10568

Middle Eastern (MID) AF: 0.500 AC: 147 AN: 294

European-Non Finnish (NFE) AF: 0.562 AC: 38177 AN: 67940

Other (OTH) AF: 0.513 AC: 1083 AN: 2112

Alfa AF: 0.532 Hom.: 12381

Bravo AF: 0.471

Asia WGS AF: 0.325 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	11
DANN	Benign	0.62
PhyloP100		2.0

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs10123308; hg19: chr9-34890139;