17-50544004-T-C

Position:

• chr17-50544004-T-C

Variant summary

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

The ENST00000504334.5(SPATA20):​c.-318+469T>C variant causes a intron, NMD transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,980 control chromosomes in the GnomAD database, including 27,059 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 0.57 (27059 hom., cov: 31)
• Consequence: SPATA20 ENST00000504334.5 intron, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566

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=-0.91).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.775 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000504334.5	c.-318+469T>C		intron_variant, NMD_transcript_variant		2		ENSP00000424215

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87162 AN: 151862 Hom.: 27029 Cov.: 31

Gnomad AFR AF: 0.782

Gnomad AMI AF: 0.717

Gnomad AMR AF: 0.462

Gnomad ASJ AF: 0.670

Gnomad EAS AF: 0.0771

Gnomad SAS AF: 0.290

Gnomad FIN AF: 0.429

Gnomad MID AF: 0.579

Gnomad NFE AF: 0.546

Gnomad OTH AF: 0.570

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.574 AC: 87235 AN: 151980 Hom.: 27059 Cov.: 31 AF XY: 0.558 AC XY: 41475 AN XY: 74284

Gnomad4 AFR AF: 0.782

Gnomad4 AMR AF: 0.462

Gnomad4 ASJ AF: 0.670

Gnomad4 EAS AF: 0.0772

Gnomad4 SAS AF: 0.289

Gnomad4 FIN AF: 0.429

Gnomad4 NFE AF: 0.546

Gnomad4 OTH AF: 0.565

Alfa AF: 0.549 Hom.: 29901

Bravo AF: 0.589

Asia WGS AF: 0.223 AC: 778 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
CADD	Benign	0.77
DANN	Benign	0.55

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1122634; hg19: chr17-48621365;