1-48268994-G-A

Variant names:

• chr1-48268994-G-A
• rs212968
• XM_006710699.4:c.1287-7326C>T

Variant summary

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

The XM_006710699.4(SPATA6):​c.1287-7326C>T 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 151,892 control chromosomes in the GnomAD database, including 26,144 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 (26144 hom., cov: 31)
• Consequence: SPATA6 XM_006710699.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.23
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.98).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.766 is higher than 0.05.

Variant Effect in Transcripts

 

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
There are no transcript annotations for this variant.

Frequencies

GnomAD3 genomes AF: 0.574 AC: 87132 AN: 151774 Hom.: 26127 Cov.: 31

Gnomad AFR AF: 0.383

Gnomad AMI AF: 0.657

Gnomad AMR AF: 0.585

Gnomad ASJ AF: 0.698

Gnomad EAS AF: 0.786

Gnomad SAS AF: 0.590

Gnomad FIN AF: 0.654

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.650

Gnomad OTH AF: 0.604

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

GnomAD4 genome AF: 0.574 AC: 87185 AN: 151892 Hom.: 26144 Cov.: 31 AF XY: 0.578 AC XY: 42862 AN XY: 74196

African (AFR) AF: 0.383 AC: 15865 AN: 41422

American (AMR) AF: 0.585 AC: 8940 AN: 15274

Ashkenazi Jewish (ASJ) AF: 0.698 AC: 2422 AN: 3470

East Asian (EAS) AF: 0.786 AC: 4062 AN: 5166

South Asian (SAS) AF: 0.589 AC: 2834 AN: 4814

European-Finnish (FIN) AF: 0.654 AC: 6886 AN: 10534

Middle Eastern (MID) AF: 0.609 AC: 179 AN: 294

European-Non Finnish (NFE) AF: 0.650 AC: 44120 AN: 67898

Other (OTH) AF: 0.606 AC: 1279 AN: 2110

Alfa AF: 0.598 Hom.: 4909

Bravo AF: 0.562

Asia WGS AF: 0.688 AC: 2388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.20
DANN	Benign	0.20
PhyloP100		-1.2

Splicing

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

Other links and lift over

dbSNP: rs212968; hg19: chr1-48734666;