rs169877

chr1-48261380-G-A

Variant summary

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

The 1-48261380-G-A 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:):

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/exons	MANE	UniProt
SPATA6	XM_006710699.4			downstream_gene_variant
SPATA6	XM_047422901.1			downstream_gene_variant
SPATA6	XM_047422913.1			downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	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;