rs12943759

Variant names:

• chr17-50548182-G-A
• rs12943759
• NM_022827.4:c.126-101G>A

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 9 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 -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 rank	MANE	Protein	UniProt
SPATA20	NM_022827.4	c.126-101G>A		intron_variant	Intron 2 of 16	ENST00000006658.11	NP_073738.2
SPATA20	NM_001258372.2	c.78-101G>A		intron_variant	Intron 1 of 15		NP_001245301.1
SPATA20	NM_001258373.2	c.-55-101G>A		intron_variant	Intron 2 of 16		NP_001245302.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000006658.11	c.126-101G>A		intron_variant	Intron 2 of 16	1	NM_022827.4	ENSP00000006658.6

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

GnomAD2 exomes AF: 0.407 AC: 49361 AN: 121224 AF XY: 0.413

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 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

African (AFR) AF: 0.154 AC: 4700 AN: 30572

American (AMR) AF: 0.381 AC: 11557 AN: 30314

Ashkenazi Jewish (ASJ) AF: 0.328 AC: 7026 AN: 21440

East Asian (EAS) AF: 0.855 AC: 30946 AN: 36180

South Asian (SAS) AF: 0.485 AC: 34879 AN: 71916

European-Finnish (FIN) AF: 0.343 AC: 13719 AN: 39986

Middle Eastern (MID) AF: 0.371 AC: 2026 AN: 5454

European-Non Finnish (NFE) AF: 0.342 AC: 363621 AN: 1063774

Other (OTH) AF: 0.367 AC: 20662 AN: 56270

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

African (AFR) AF: 0.160 AC: 6627 AN: 41450

American (AMR) AF: 0.364 AC: 5552 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.323 AC: 1121 AN: 3470

East Asian (EAS) AF: 0.841 AC: 4346 AN: 5170

South Asian (SAS) AF: 0.486 AC: 2343 AN: 4818

European-Finnish (FIN) AF: 0.342 AC: 3619 AN: 10570

Middle Eastern (MID) AF: 0.347 AC: 102 AN: 294

European-Non Finnish (NFE) AF: 0.345 AC: 23467 AN: 67944

Other (OTH) AF: 0.336 AC: 710 AN: 2114

Alfa AF: 0.328 Hom.: 2356

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
PhyloP100		0.87
PromoterAI		-0.015	Neutral
RBP_binding_hub_radar		0.0
RBP_regulation_power_radar		1.1
Mutation Taster		=100/0	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: rs12943759; hg19: chr17-48625543;