rs12943759

Positions:

• chr17-50548182-G-A
• chr17-50548182-G-C

Variant summary

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

The NM_022827.4(SPATA20):​c.126-101G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.356 in 1,507,908 control chromosomes in the GnomAD database, including 103,635 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 0.32 (8950 hom., cov: 32)
  • Exomes 𝑓: 0.36 (94685 hom.)
• Consequence: SPATA20 NM_022827.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.869

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 (BayesDel_noAF=-0.83).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.82 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA20	NM_022827.4	c.126-101G>A		intron_variant		ENST00000006658.11	NP_073738.2
SPATA20	NM_001258372.2	c.78-101G>A		intron_variant			NP_001245301.1
SPATA20	NM_001258373.2	c.-55-101G>A		intron_variant			NP_001245302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000006658.11	c.126-101G>A		intron_variant		1	NM_022827.4	ENSP00000006658

Frequencies

GnomAD3 genomes AF: 0.317 AC: 48123 AN: 151884 Hom.: 8951 Cov.: 32

Gnomad AFR AF: 0.160

Gnomad AMI AF: 0.260

Gnomad AMR AF: 0.364

Gnomad ASJ AF: 0.323

Gnomad EAS AF: 0.841

Gnomad SAS AF: 0.486

Gnomad FIN AF: 0.342

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.345

Gnomad OTH AF: 0.341

GnomAD3 exomes AF: 0.407 AC: 49361 AN: 121224 Hom.: 11618 AF XY: 0.413 AC XY: 26296 AN XY: 63718

Gnomad AFR exome AF: 0.157

Gnomad AMR exome AF: 0.384

Gnomad ASJ exome AF: 0.338

Gnomad EAS exome AF: 0.850

Gnomad SAS exome AF: 0.500

Gnomad FIN exome AF: 0.350

Gnomad NFE exome AF: 0.347

Gnomad OTH exome AF: 0.385

GnomAD4 exome AF: 0.361 AC: 489136 AN: 1355906 Hom.: 94685 Cov.: 46 AF XY: 0.364 AC XY: 242371 AN XY: 665852

Gnomad4 AFR exome AF: 0.154

Gnomad4 AMR exome AF: 0.381

Gnomad4 ASJ exome AF: 0.328

Gnomad4 EAS exome AF: 0.855

Gnomad4 SAS exome AF: 0.485

Gnomad4 FIN exome AF: 0.343

Gnomad4 NFE exome AF: 0.342

Gnomad4 OTH exome AF: 0.367

GnomAD4 genome AF: 0.317 AC: 48124 AN: 152002 Hom.: 8950 Cov.: 32 AF XY: 0.323 AC XY: 23995 AN XY: 74298

Gnomad4 AFR AF: 0.160

Gnomad4 AMR AF: 0.364

Gnomad4 ASJ AF: 0.323

Gnomad4 EAS AF: 0.841

Gnomad4 SAS AF: 0.486

Gnomad4 FIN AF: 0.342

Gnomad4 NFE AF: 0.345

Gnomad4 OTH AF: 0.336

Alfa AF: 0.331 Hom.: 2345

Bravo AF: 0.311

Asia WGS AF: 0.592 AC: 2057 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.6
DANN	Benign	0.36
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1

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: rs12943759; hg19: chr17-48625543;