17-50544004-T-C

Variant names:

• chr17-50544004-T-C
• rs1122634
• ENST00000504334.5:n.-318+469T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000504334.5(SPATA20):​n.-318+469T>C variant causes a intron 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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.566
• Publications: 19 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=-0.91).
• 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 rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA20	ENST00000504334.5	n.-318+469T>C		intron_variant	Intron 1 of 17	2		ENSP00000424215.1

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

African (AFR) AF: 0.782 AC: 32379 AN: 41418

American (AMR) AF: 0.462 AC: 7063 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.670 AC: 2325 AN: 3468

East Asian (EAS) AF: 0.0772 AC: 399 AN: 5166

South Asian (SAS) AF: 0.289 AC: 1391 AN: 4812

European-Finnish (FIN) AF: 0.429 AC: 4532 AN: 10558

Middle Eastern (MID) AF: 0.592 AC: 174 AN: 294

European-Non Finnish (NFE) AF: 0.546 AC: 37128 AN: 67956

Other (OTH) AF: 0.565 AC: 1190 AN: 2108

Alfa AF: 0.556 Hom.: 38987

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
PhyloP100		-0.57

Splicing

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

Other links and lift over

dbSNP: rs1122634; hg19: chr17-48621365;