rs12085824

chr1-48342131-A-G

Variant summary

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

The NM_019073.4(SPATA6):c.1194+13539T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 152,092 control chromosomes in the GnomAD database, including 12,883 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 0.40 (12883 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.222

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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA6	NM_019073.4	c.1194+13539T>C		intron_variant		ENST00000371847.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA6	ENST00000371847.8	c.1194+13539T>C		intron_variant		1	NM_019073.4	P4

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60843 AN: 151974 Hom.: 12864 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.343

Gnomad AMR AF: 0.403

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.188

Gnomad SAS AF: 0.362

Gnomad FIN AF: 0.320

Gnomad MID AF: 0.399

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.376

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

GnomAD4 genome AF: 0.400 AC: 60898 AN: 152092 Hom.: 12883 Cov.: 32 AF XY: 0.395 AC XY: 29377 AN XY: 74356

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.403

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.188

Gnomad4 SAS AF: 0.363

Gnomad4 FIN AF: 0.320

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.374

Alfa AF: 0.355 Hom.: 5170

Bravo AF: 0.412

Asia WGS AF: 0.279 AC: 972 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	5.0
Dann	Benign	0.67

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs12085824; hg19: chr1-48807803; COSMIC: COSV64056749; COSMIC: COSV64056749;