rs3738309

chr1-48403616-T-A

Variant summary

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

The NM_019073.4(SPATA6):c.486+186A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.31 in 151,914 control chromosomes in the GnomAD database, including 8,970 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 0.31 (8970 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.160

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=-0.82).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.414 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA6	NM_019073.4	c.486+186A>T		intron_variant		ENST00000371847.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA6	ENST00000371847.8	c.486+186A>T		intron_variant		1	NM_019073.4	P4

Frequencies

GnomAD3 genomes AF: 0.310 AC: 47128 AN: 151796 Hom.: 8962 Cov.: 32

Gnomad AFR AF: 0.0773

Gnomad AMI AF: 0.400

Gnomad AMR AF: 0.351

Gnomad ASJ AF: 0.467

Gnomad EAS AF: 0.352

Gnomad SAS AF: 0.358

Gnomad FIN AF: 0.364

Gnomad MID AF: 0.417

Gnomad NFE AF: 0.418

Gnomad OTH AF: 0.333

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

GnomAD4 genome AF: 0.310 AC: 47137 AN: 151914 Hom.: 8970 Cov.: 32 AF XY: 0.312 AC XY: 23163 AN XY: 74232

Gnomad4 AFR AF: 0.0771

Gnomad4 AMR AF: 0.352

Gnomad4 ASJ AF: 0.467

Gnomad4 EAS AF: 0.352

Gnomad4 SAS AF: 0.358

Gnomad4 FIN AF: 0.364

Gnomad4 NFE AF: 0.418

Gnomad4 OTH AF: 0.331

Alfa AF: 0.365 Hom.: 1404

Bravo AF: 0.298

Asia WGS AF: 0.376 AC: 1306 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
Cadd	Benign	5.3
Dann	Benign	0.74

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: rs3738309; hg19: chr1-48869288;