1-48413132-C-T

Variant summary

Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_Moderate BP6_Moderate BP7

The NM_019073.4(SPATA6):c.258G>A(p.Glu86=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0023 in 1,399,952 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

• Frequency:
  • Genomes: 𝑓 0.0014 (0 hom., cov: 32)
  • Exomes 𝑓: 0.0024 (4 hom.)
• Consequence: SPATA6 NM_019073.4 synonymous
• Clinical Significance: Benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 2.02

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 Likely_benign. Variant got -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.32).
• BP6: Variant 1-48413132-C-T is Benign according to our data. Variant chr1-48413132-C-T is described in ClinVar as [Benign]. Clinvar id is 716829.Status of the report is criteria_provided_single_submitter, 1 stars.
• BP7: Synonymous conserved (PhyloP=2.02 with no splicing effect.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA6	NM_019073.4	c.258G>A	p.Glu86=	synonymous_variant	4/13	ENST00000371847.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA6	ENST00000371847.8	c.258G>A	p.Glu86=	synonymous_variant	4/13	1	NM_019073.4	P4

Frequencies

GnomAD3 genomes AF: 0.00137 AC: 206 AN: 150614 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000535

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000730

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.000101

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.00252

Gnomad OTH AF: 0.000483

GnomAD3 exomes AF: 0.00123 AC: 167 AN: 136218 Hom.: 0 AF XY: 0.00117 AC XY: 90 AN XY: 76934

Gnomad AFR exome AF: 0.000692

Gnomad AMR exome AF: 0.000894

Gnomad ASJ exome AF: 0.000176

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.00215

Gnomad OTH exome AF: 0.00114

GnomAD4 exome AF: 0.00241 AC: 3013 AN: 1249274 Hom.: 4 Cov.: 20 AF XY: 0.00233 AC XY: 1441 AN XY: 617360

Gnomad4 AFR exome AF: 0.000620

Gnomad4 AMR exome AF: 0.000981

Gnomad4 ASJ exome AF: 0.000101

Gnomad4 EAS exome AF: 0.000137

Gnomad4 SAS exome AF: 0.0000749

Gnomad4 FIN exome AF: 0.0000457

Gnomad4 NFE exome AF: 0.00283

Gnomad4 OTH exome AF: 0.00236

GnomAD4 genome AF: 0.00137 AC: 206 AN: 150678 Hom.: 0 Cov.: 32 AF XY: 0.00110 AC XY: 81 AN XY: 73610

Gnomad4 AFR AF: 0.000533

Gnomad4 AMR AF: 0.000729

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.000101

Gnomad4 NFE AF: 0.00252

Gnomad4 OTH AF: 0.000479

Alfa AF: 0.00173 Hom.: 1

Bravo AF: 0.00156

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Benign, criteria provided, single submitter

clinical testing

Invitae

Jul 16, 2018

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Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.32
Cadd	Benign	8.2
Dann	Benign	0.39

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.040		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: rs150265971; hg19: chr1-48878804; COSMIC: COSV64062883;