rs10123308

Positions:

• chr9-34890142-A-G
• chr9-34890142-A-T

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]

(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
SPATA31F3	ENST00000340783.11	c.359-510T>C		intron_variant		4	NM_001309427.2	ENSP00000489571
	ENST00000658462.1	n.216+488A>G		intron_variant, non_coding_transcript_variant
SPATA31F3	ENST00000603592.1	c.355-507T>C		intron_variant		3		ENSP00000489523
SPATA31F3	ENST00000603640.6	c.746-507T>C		intron_variant		5		ENSP00000489585	P1

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;