rs1132414

chr17-50550731-A-G

Variant summary

Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_022827.4(SPATA20):c.1197A>G(p.Glu399=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.256 in 1,613,106 control chromosomes in the GnomAD database, including 61,124 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 0.35 (11558 hom., cov: 34)
  • Exomes 𝑓: 0.25 (49566 hom.)
• Consequence: SPATA20 NM_022827.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72

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 -13 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.52).
• BP7: Synonymous conserved (PhyloP=1.72 with no splicing effect.
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.616 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA20	NM_022827.4	c.1197A>G	p.Glu399=	synonymous_variant	11/17	ENST00000006658.11
SPATA20	NM_001258372.2	c.1149A>G	p.Glu383=	synonymous_variant	10/16
SPATA20	NM_001258373.2	c.1017A>G	p.Glu339=	synonymous_variant	11/17

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA20	ENST00000006658.11	c.1197A>G	p.Glu399=	synonymous_variant	11/17	1	NM_022827.4

Frequencies

GnomAD3 genomes AF: 0.346 AC: 52655 AN: 152136 Hom.: 11539 Cov.: 34

Gnomad AFR AF: 0.622

Gnomad AMI AF: 0.486

Gnomad AMR AF: 0.278

Gnomad ASJ AF: 0.379

Gnomad EAS AF: 0.0523

Gnomad SAS AF: 0.144

Gnomad FIN AF: 0.231

Gnomad MID AF: 0.288

Gnomad NFE AF: 0.245

Gnomad OTH AF: 0.338

GnomAD3 exomes AF: 0.247 AC: 61889 AN: 250514 Hom.: 9617 AF XY: 0.239 AC XY: 32403 AN XY: 135678

Gnomad AFR exome AF: 0.628

Gnomad AMR exome AF: 0.210

Gnomad ASJ exome AF: 0.396

Gnomad EAS exome AF: 0.0491

Gnomad SAS exome AF: 0.141

Gnomad FIN exome AF: 0.231

Gnomad NFE exome AF: 0.254

Gnomad OTH exome AF: 0.261

GnomAD4 exome AF: 0.247 AC: 360950 AN: 1460852 Hom.: 49566 Cov.: 37 AF XY: 0.243 AC XY: 176655 AN XY: 726714

Gnomad4 AFR exome AF: 0.639

Gnomad4 AMR exome AF: 0.216

Gnomad4 ASJ exome AF: 0.389

Gnomad4 EAS exome AF: 0.0487

Gnomad4 SAS exome AF: 0.144

Gnomad4 FIN exome AF: 0.235

Gnomad4 NFE exome AF: 0.247

Gnomad4 OTH exome AF: 0.272

GnomAD4 genome AF: 0.346 AC: 52711 AN: 152254 Hom.: 11558 Cov.: 34 AF XY: 0.340 AC XY: 25272 AN XY: 74428

Gnomad4 AFR AF: 0.622

Gnomad4 AMR AF: 0.278

Gnomad4 ASJ AF: 0.379

Gnomad4 EAS AF: 0.0522

Gnomad4 SAS AF: 0.144

Gnomad4 FIN AF: 0.231

Gnomad4 NFE AF: 0.245

Gnomad4 OTH AF: 0.334

Alfa AF: 0.276 Hom.: 9738

Bravo AF: 0.365

Asia WGS AF: 0.139 AC: 484 AN: 3478

EpiCase AF: 0.267

EpiControl AF: 0.262

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.52
Cadd	Benign	2.0
Dann	Benign	0.72

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: rs1132414; hg19: chr17-48628092; COSMIC: COSV50065725; COSMIC: COSV50065725;