9-34890142-A-G

Position:

• chr9-34890142-A-G

Variant summary

Our verdict is Benign. Variant got -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

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]

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]

ENSG00000287368 (HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA31F3	NM_001309427.2	c.359-510T>C		intron_variant		ENST00000340783.11	NP_001296356.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
FAM205C	ENST00000340783.11	c.359-510T>C		intron_variant		4	NM_001309427.2	ENSP00000489571.1
FAM205C	ENST00000603640.6	c.746-507T>C		intron_variant		5		ENSP00000489585.1
FAM205C	ENST00000603592.1	c.355-507T>C		intron_variant		3		ENSP00000489523.1
ENSG00000287368	ENST00000658462.1	n.216+488A>G		intron_variant

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

Gnomad4 AFR AF: 0.318

Gnomad4 AMR AF: 0.530

Gnomad4 ASJ AF: 0.508

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.316

Gnomad4 FIN AF: 0.549

Gnomad4 NFE AF: 0.562

Gnomad4 OTH AF: 0.513

Alfa AF: 0.532 Hom.: 11108

Bravo AF: 0.471

Asia WGS AF: 0.325 AC: 1134 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

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

Publications

LitVar

Other links and lift over

dbSNP: rs10123308; hg19: chr9-34890139;