rs12085605

chr1-48318737-C-G

Variant summary

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

The NM_019073.4(SPATA6):c.1195-12859G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.144 in 152,044 control chromosomes in the GnomAD database, including 1,775 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 0.14 (1775 hom., cov: 33)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20

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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA6	NM_019073.4	c.1195-12859G>C		intron_variant		ENST00000371847.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA6	ENST00000371847.8	c.1195-12859G>C		intron_variant		1	NM_019073.4	P4

Frequencies

GnomAD3 genomes AF: 0.144 AC: 21825 AN: 151924 Hom.: 1775 Cov.: 33

Gnomad AFR AF: 0.207

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.102

Gnomad ASJ AF: 0.132

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0921

Gnomad MID AF: 0.158

Gnomad NFE AF: 0.132

Gnomad OTH AF: 0.137

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

GnomAD4 genome AF: 0.144 AC: 21836 AN: 152044 Hom.: 1775 Cov.: 33 AF XY: 0.141 AC XY: 10480 AN XY: 74318

Gnomad4 AFR AF: 0.207

Gnomad4 AMR AF: 0.101

Gnomad4 ASJ AF: 0.132

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.0921

Gnomad4 NFE AF: 0.132

Gnomad4 OTH AF: 0.135

Alfa AF: 0.142 Hom.: 201

Bravo AF: 0.145

Asia WGS AF: 0.0900 AC: 313 AN: 3464

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	2.0
Dann	Benign	0.62

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: rs12085605; hg19: chr1-48784409;