rs169877

Variant names:

• chr1-48261380-G-A
• rs169877
• ENST00000833424.1:n.*9C>T

Variant summary

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

The ENST00000833424.1(ENSG00000308343):​n.*9C>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: ENSG00000308343 ENST00000833424.1 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.700
• Publications: 4 publications found

Genes affected

ENSG00000308343 (HGNC:):

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

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000833424.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ENSG00000308343	ENST00000833424.1		n.*9C>T		downstream_gene	N/A

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

African (AFR) AF: 0.382 AC: 15843 AN: 41424

American (AMR) AF: 0.585 AC: 8927 AN: 15250

Ashkenazi Jewish (ASJ) AF: 0.691 AC: 2396 AN: 3468

East Asian (EAS) AF: 0.787 AC: 4073 AN: 5174

South Asian (SAS) AF: 0.589 AC: 2838 AN: 4820

European-Finnish (FIN) AF: 0.654 AC: 6915 AN: 10578

Middle Eastern (MID) AF: 0.602 AC: 177 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44090 AN: 67866

Other (OTH) AF: 0.605 AC: 1277 AN: 2110

Alfa AF: 0.608 Hom.: 11116

Bravo AF: 0.562

Asia WGS AF: 0.688 AC: 2390 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	5.4
DANN	Benign	0.68
PhyloP100		0.70

Splicing

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

Other links and lift over

dbSNP: rs169877; hg19: chr1-48727052;