rs12085605

Variant names:

• chr1-48318737-C-G
• rs12085605
• NM_019073.4:c.1195-12859G>C

Variant summary

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

The ENST00000371847.8(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 ENST00000371847.8 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.20
• Publications: 2 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=-0.84).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.203 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000371847.8. 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
	SPATA6	NM_019073.4	MANE Select	c.1195-12859G>C		intron	N/A	NP_061946.1
	SPATA6	NM_001286239.2		c.1153-12859G>C		intron	N/A	NP_001273168.1
	SPATA6	NM_001286238.2		c.1147-12859G>C		intron	N/A	NP_001273167.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA6	ENST00000371847.8	TSL:1 MANE Select	c.1195-12859G>C		intron	N/A	ENSP00000360913.3
	SPATA6	ENST00000371843.7	TSL:1	c.1147-12859G>C		intron	N/A	ENSP00000360909.3
	SPATA6	ENST00000396199.7	TSL:2	c.1153-12859G>C		intron	N/A	ENSP00000379502.4

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

African (AFR) AF: 0.207 AC: 8583 AN: 41460

American (AMR) AF: 0.101 AC: 1549 AN: 15286

Ashkenazi Jewish (ASJ) AF: 0.132 AC: 459 AN: 3470

East Asian (EAS) AF: 0.0108 AC: 56 AN: 5188

South Asian (SAS) AF: 0.171 AC: 827 AN: 4824

European-Finnish (FIN) AF: 0.0921 AC: 974 AN: 10570

Middle Eastern (MID) AF: 0.156 AC: 46 AN: 294

European-Non Finnish (NFE) AF: 0.132 AC: 8942 AN: 67926

Other (OTH) AF: 0.135 AC: 286 AN: 2114

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
CADD	Benign	2.0
DANN	Benign	0.62
PhyloP100		-1.2
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs12085605; hg19: chr1-48784409;