rs169877

Variant names:

• chr1-48261380-G-A
• rs169877
• XM_006710699.4:c.*264C>T

Variant summary

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

The XM_006710699.4(SPATA6):​c.*264C>T variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.574 in 151,894 control chromosomes in the GnomAD database, including 26,120 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 (26120 hom., cov: 33)
• Consequence: SPATA6 XM_006710699.4 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700

Genes affected

SPATA6 (HGNC:18309): (spermatogenesis associated 6) Predicted to enable myosin light chain binding activity. Predicted to be involved in motile cilium assembly and spermatogenesis. Predicted to be located in extracellular region. Predicted to be active in sperm connecting piece. [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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.767 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA6	XM_006710699.4	c.*264C>T		downstream_gene_variant			XP_006710762.1
SPATA6	XM_047422901.1	c.*264C>T		downstream_gene_variant			XP_047278857.1
SPATA6	XM_047422913.1	c.*264C>T		downstream_gene_variant			XP_047278869.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87081 AN: 151776 Hom.: 26103 Cov.: 33

Gnomad AFR AF: 0.382

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.691

Gnomad EAS AF: 0.787

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.589

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.603

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

GnomAD4 genome AF: 0.574 AC: 87134 AN: 151894 Hom.: 26120 Cov.: 33 AF XY: 0.578 AC XY: 42899 AN XY: 74276

Gnomad4 AFR AF: 0.382

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.691

Gnomad4 EAS AF: 0.787

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.605

Alfa AF: 0.612 Hom.: 8873

Bravo AF: 0.562

Asia WGS AF: 0.688 AC: 2390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
DANN	Benign	0.68

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs169877; hg19: chr1-48727052;