rs932087

Positions:

• chr1-48358484-A-T

Variant summary

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

The NM_019073.4(SPATA6):​c.1094+1102T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.098 in 152,100 control chromosomes in the GnomAD database, including 877 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 0.098 (877 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.590

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=-0.89).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.161 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA6	NM_019073.4	c.1094+1102T>A		intron_variant		ENST00000371847.8	NP_061946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA6	ENST00000371847.8	c.1094+1102T>A		intron_variant		1	NM_019073.4	ENSP00000360913	P4

Frequencies

GnomAD3 genomes AF: 0.0981 AC: 14911 AN: 151982 Hom.: 878 Cov.: 32

Gnomad AFR AF: 0.0513

Gnomad AMI AF: 0.125

Gnomad AMR AF: 0.0826

Gnomad ASJ AF: 0.129

Gnomad EAS AF: 0.0110

Gnomad SAS AF: 0.170

Gnomad FIN AF: 0.0917

Gnomad MID AF: 0.121

Gnomad NFE AF: 0.130

Gnomad OTH AF: 0.104

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

GnomAD4 genome AF: 0.0980 AC: 14913 AN: 152100 Hom.: 877 Cov.: 32 AF XY: 0.0964 AC XY: 7166 AN XY: 74350

Gnomad4 AFR AF: 0.0513

Gnomad4 AMR AF: 0.0824

Gnomad4 ASJ AF: 0.129

Gnomad4 EAS AF: 0.0108

Gnomad4 SAS AF: 0.171

Gnomad4 FIN AF: 0.0917

Gnomad4 NFE AF: 0.130

Gnomad4 OTH AF: 0.102

Alfa AF: 0.115 Hom.: 131

Bravo AF: 0.0929

Asia WGS AF: 0.0830 AC: 290 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	1.4
DANN	Benign	0.46

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: rs932087; hg19: chr1-48824156;