rs16921669

chr9-4635232-G-Achr9-4635232-G-C

Variant summary

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

The NM_001353486.2(SPATA6L):c.351+43C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.077 in 1,469,260 control chromosomes in the GnomAD database, including 8,194 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 (2189 hom., cov: 32)
  • Exomes 𝑓: 0.070 (6005 hom.)
• Consequence: SPATA6L NM_001353486.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.757

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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.32 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA6L	NM_001353486.2	c.351+43C>T		intron_variant		ENST00000682582.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA6L	ENST00000682582.1	c.351+43C>T		intron_variant			NM_001353486.2

Frequencies

GnomAD3 genomes AF: 0.136 AC: 20618 AN: 151886 Hom.: 2176 Cov.: 32

Gnomad AFR AF: 0.274

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.137

Gnomad ASJ AF: 0.0548

Gnomad EAS AF: 0.334

Gnomad SAS AF: 0.113

Gnomad FIN AF: 0.0686

Gnomad MID AF: 0.0949

Gnomad NFE AF: 0.0550

Gnomad OTH AF: 0.101

GnomAD3 exomes AF: 0.102 AC: 14097 AN: 137746 Hom.: 1251 AF XY: 0.0942 AC XY: 7187 AN XY: 76272

Gnomad AFR exome AF: 0.281

Gnomad AMR exome AF: 0.158

Gnomad ASJ exome AF: 0.0529

Gnomad EAS exome AF: 0.332

Gnomad SAS exome AF: 0.101

Gnomad FIN exome AF: 0.0678

Gnomad NFE exome AF: 0.0560

Gnomad OTH exome AF: 0.0846

GnomAD4 exome AF: 0.0702 AC: 92445 AN: 1317256 Hom.: 6005 Cov.: 30 AF XY: 0.0694 AC XY: 44845 AN XY: 646142

Gnomad4 AFR exome AF: 0.284

Gnomad4 AMR exome AF: 0.151

Gnomad4 ASJ exome AF: 0.0610

Gnomad4 EAS exome AF: 0.389

Gnomad4 SAS exome AF: 0.0931

Gnomad4 FIN exome AF: 0.0699

Gnomad4 NFE exome AF: 0.0515

Gnomad4 OTH exome AF: 0.0907

GnomAD4 genome AF: 0.136 AC: 20670 AN: 152004 Hom.: 2189 Cov.: 32 AF XY: 0.136 AC XY: 10136 AN XY: 74290

Gnomad4 AFR AF: 0.274

Gnomad4 AMR AF: 0.137

Gnomad4 ASJ AF: 0.0548

Gnomad4 EAS AF: 0.333

Gnomad4 SAS AF: 0.112

Gnomad4 FIN AF: 0.0686

Gnomad4 NFE AF: 0.0551

Gnomad4 OTH AF: 0.106

Alfa AF: 0.0725 Hom.: 1336

Bravo AF: 0.148

Asia WGS AF: 0.249 AC: 864 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
Cadd	Benign	6.0
Dann	Benign	0.73

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: rs16921669; hg19: chr9-4635232; COSMIC: COSV56305563; COSMIC: COSV56305563;