rs212968

Positions:

• chr1-48268994-G-A
• chr1-48268994-G-C
• chr1-48268994-G-T

Variant summary

Our verdict is Benign. Variant got -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

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA6	XM_006710699.4	c.1287-7326C>T		intron_variant			XP_006710762.1
SPATA6	XM_047422901.1	c.1239-7326C>T		intron_variant			XP_047278857.1
SPATA6	XM_047422913.1	c.1002-7326C>T		intron_variant			XP_047278869.1
		n.48268994G>A		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt

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

Gnomad4 AFR AF: 0.383

Gnomad4 AMR AF: 0.585

Gnomad4 ASJ AF: 0.698

Gnomad4 EAS AF: 0.786

Gnomad4 SAS AF: 0.589

Gnomad4 FIN AF: 0.654

Gnomad4 NFE AF: 0.650

Gnomad4 OTH AF: 0.606

Alfa AF: 0.604 Hom.: 4836

Bravo AF: 0.562

Asia WGS AF: 0.688 AC: 2388 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

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

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs212968; hg19: chr1-48734666;