rs9913430

Variant names:

• chr17-50551109-T-A
• rs9913430
• NM_022827.4:c.1495T>A

Variant summary

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

The NM_022827.4(SPATA20):​c.1495T>A​(p.Ser499Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.285 in 1,612,064 control chromosomes in the GnomAD database, including 75,652 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.39 (14902 hom., cov: 33)
  • Exomes 𝑓: 0.27 (60750 hom.)
• Consequence: SPATA20 NM_022827.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.106

Genes affected

SPATA20 (HGNC:26125): (spermatogenesis associated 20) Predicted to be involved in carbohydrate metabolic process; cell differentiation; and spermatogenesis. Predicted to be located in extracellular region. [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 (MetaRNN=3.3013168E-6).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.693 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA20	NM_022827.4	c.1495T>A	p.Ser499Thr	missense_variant	Exon 12 of 17	ENST00000006658.11	NP_073738.2
SPATA20	NM_001258372.2	c.1447T>A	p.Ser483Thr	missense_variant	Exon 11 of 16		NP_001245301.1
SPATA20	NM_001258373.2	c.1315T>A	p.Ser439Thr	missense_variant	Exon 12 of 17		NP_001245302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000006658.11	c.1495T>A	p.Ser499Thr	missense_variant	Exon 12 of 17	1	NM_022827.4	ENSP00000006658.6

Frequencies

GnomAD3 genomes AF: 0.394 AC: 59944 AN: 152006 Hom.: 14853 Cov.: 33

Gnomad AFR AF: 0.700

Gnomad AMI AF: 0.485

Gnomad AMR AF: 0.405

Gnomad ASJ AF: 0.428

Gnomad EAS AF: 0.103

Gnomad SAS AF: 0.180

Gnomad FIN AF: 0.256

Gnomad MID AF: 0.313

Gnomad NFE AF: 0.263

Gnomad OTH AF: 0.388

GnomAD3 exomes AF: 0.304 AC: 75382 AN: 248364 Hom.: 13803 AF XY: 0.288 AC XY: 38867 AN XY: 134988

Gnomad AFR exome AF: 0.705

Gnomad AMR exome AF: 0.421

Gnomad ASJ exome AF: 0.447

Gnomad EAS exome AF: 0.0974

Gnomad SAS exome AF: 0.176

Gnomad FIN exome AF: 0.260

Gnomad NFE exome AF: 0.273

Gnomad OTH exome AF: 0.314

GnomAD4 exome AF: 0.274 AC: 399709 AN: 1459940 Hom.: 60750 Cov.: 37 AF XY: 0.269 AC XY: 195553 AN XY: 726250

Gnomad4 AFR exome AF: 0.718

Gnomad4 AMR exome AF: 0.414

Gnomad4 ASJ exome AF: 0.439

Gnomad4 EAS exome AF: 0.0854

Gnomad4 SAS exome AF: 0.180

Gnomad4 FIN exome AF: 0.267

Gnomad4 NFE exome AF: 0.263

Gnomad4 OTH exome AF: 0.307

GnomAD4 genome AF: 0.395 AC: 60049 AN: 152124 Hom.: 14902 Cov.: 33 AF XY: 0.389 AC XY: 28942 AN XY: 74354

Gnomad4 AFR AF: 0.700

Gnomad4 AMR AF: 0.406

Gnomad4 ASJ AF: 0.428

Gnomad4 EAS AF: 0.104

Gnomad4 SAS AF: 0.180

Gnomad4 FIN AF: 0.256

Gnomad4 NFE AF: 0.263

Gnomad4 OTH AF: 0.396

Alfa AF: 0.313 Hom.: 2793

Bravo AF: 0.424

TwinsUK AF: 0.246 AC: 911

ALSPAC AF: 0.263 AC: 1013

ESP6500AA AF: 0.680 AC: 2995

ESP6500EA AF: 0.274 AC: 2359

ExAC AF: 0.303 AC: 36666

Asia WGS AF: 0.225 AC: 785 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.067
BayesDel_addAF	Benign	-0.84	T
BayesDel_noAF	Benign	-0.83
CADD	Benign	0.53
DANN	Benign	0.65
DEOGEN2	Benign	0.055	.;.;T;T
Eigen	Benign	-1.9
Eigen_PC	Benign	-1.9
FATHMM_MKL	Benign	0.077	N
LIST_S2	Benign	0.019	T;T;T;T
MetaRNN	Benign	0.0000033	T;T;T;T
MetaSVM	Benign	-1.0	T
MutationAssessor	Benign	0.045	.;.;N;.
PrimateAI	Benign	0.34	T
PROVEAN	Benign	-0.43	.;N;N;.
REVEL	Benign	0.011
Sift	Benign	0.67	.;T;T;.
Sift4G	Benign	0.57	T;T;T;T
Polyphen		0.0	.;B;B;.
Vest4		0.033
MPC		0.18
ClinPred		0.0054	T
GERP RS		-6.5
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.7
Varity_R		0.050
gMVP		0.14

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.070		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: rs9913430; hg19: chr17-48628470; COSMIC: COSV50065954; COSMIC: COSV50065954;