chr17-50550731-A-G

Variant names:

• chr17-50550731-A-G
• rs1132414
• NM_022827.4:c.1197A>G

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_Strong BP7 BA1

The NM_022827.4(SPATA20):​c.1197A>G​(p.Glu399Glu) 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
• Publications: 22 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SPATA20	NM_022827.4	c.1197A>G	p.Glu399Glu	synonymous_variant	Exon 11 of 17	ENST00000006658.11	NP_073738.2
SPATA20	NM_001258372.2	c.1149A>G	p.Glu383Glu	synonymous_variant	Exon 10 of 16		NP_001245301.1
SPATA20	NM_001258373.2	c.1017A>G	p.Glu339Glu	synonymous_variant	Exon 11 of 17		NP_001245302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000006658.11	c.1197A>G	p.Glu399Glu	synonymous_variant	Exon 11 of 17	1	NM_022827.4	ENSP00000006658.6

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

GnomAD2 exomes AF: 0.247 AC: 61889 AN: 250514 AF XY: 0.239

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 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

African (AFR) AF: 0.639 AC: 21377 AN: 33478

American (AMR) AF: 0.216 AC: 9669 AN: 44720

Ashkenazi Jewish (ASJ) AF: 0.389 AC: 10163 AN: 26132

East Asian (EAS) AF: 0.0487 AC: 1933 AN: 39700

South Asian (SAS) AF: 0.144 AC: 12443 AN: 86254

European-Finnish (FIN) AF: 0.235 AC: 12357 AN: 52550

Middle Eastern (MID) AF: 0.312 AC: 1800 AN: 5768

European-Non Finnish (NFE) AF: 0.247 AC: 274759 AN: 1111868

Other (OTH) AF: 0.272 AC: 16449 AN: 60382

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

African (AFR) AF: 0.622 AC: 25844 AN: 41544

American (AMR) AF: 0.278 AC: 4250 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.379 AC: 1316 AN: 3472

East Asian (EAS) AF: 0.0522 AC: 271 AN: 5188

South Asian (SAS) AF: 0.144 AC: 694 AN: 4828

European-Finnish (FIN) AF: 0.231 AC: 2449 AN: 10596

Middle Eastern (MID) AF: 0.289 AC: 85 AN: 294

European-Non Finnish (NFE) AF: 0.245 AC: 16653 AN: 68008

Other (OTH) AF: 0.334 AC: 706 AN: 2112

Alfa AF: 0.283 Hom.: 26225

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
PhyloP100		1.7
Mutation Taster		=99/1	polymorphism (auto)

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