rs384535

chr9-4625995-T-C

Variant summary

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

The NM_001353486.2(SPATA6L):c.430-429A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 156,652 control chromosomes in the GnomAD database, including 1,255 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 0.12 (1244 hom., cov: 32)
  • Exomes 𝑓: 0.070 (11 hom.)
• Consequence: SPATA6L NM_001353486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0300

Genes affected

SPATA6L (HGNC:25472): (spermatogenesis associated 6 like) Predicted to enable myosin light chain binding activity. Predicted to be involved in spermatogenesis. Predicted to be located 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=-0.88).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.183 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA6L	NM_001353486.2	c.430-429A>G		intron_variant		ENST00000682582.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA6L	ENST00000682582.1	c.430-429A>G		intron_variant			NM_001353486.2

Frequencies

GnomAD3 genomes AF: 0.115 AC: 17533 AN: 152020 Hom.: 1245 Cov.: 32

Gnomad AFR AF: 0.187

Gnomad AMI AF: 0.0504

Gnomad AMR AF: 0.0954

Gnomad ASJ AF: 0.116

Gnomad EAS AF: 0.0360

Gnomad SAS AF: 0.123

Gnomad FIN AF: 0.0391

Gnomad MID AF: 0.196

Gnomad NFE AF: 0.0939

Gnomad OTH AF: 0.127

GnomAD4 exome AF: 0.0700 AC: 316 AN: 4514 Hom.: 11 Cov.: 0 AF XY: 0.0704 AC XY: 180 AN XY: 2558

Gnomad4 AFR exome AF: 0.0333

Gnomad4 AMR exome AF: 0.0641

Gnomad4 ASJ exome AF: 0.0667

Gnomad4 EAS exome AF: 0.00685

Gnomad4 SAS exome AF: 0.0862

Gnomad4 FIN exome AF: 0.0417

Gnomad4 NFE exome AF: 0.0732

Gnomad4 OTH exome AF: 0.0691

GnomAD4 genome AF: 0.115 AC: 17541 AN: 152138 Hom.: 1244 Cov.: 32 AF XY: 0.113 AC XY: 8440 AN XY: 74386

Gnomad4 AFR AF: 0.187

Gnomad4 AMR AF: 0.0951

Gnomad4 ASJ AF: 0.116

Gnomad4 EAS AF: 0.0363

Gnomad4 SAS AF: 0.122

Gnomad4 FIN AF: 0.0391

Gnomad4 NFE AF: 0.0938

Gnomad4 OTH AF: 0.128

Alfa AF: 0.108 Hom.: 259

Bravo AF: 0.120

Asia WGS AF: 0.107 AC: 373 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
Cadd	Benign	3.4
Dann	Benign	0.78

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: rs384535; hg19: chr9-4625995;