rs11205476

chr1-48354622-C-T

Variant summary

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

The NM_019073.4(SPATA6):c.1194+1048G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.427 in 151,866 control chromosomes in the GnomAD database, including 14,931 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 0.43 (14931 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.202

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=-0.96).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.611 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA6	NM_019073.4	c.1194+1048G>A		intron_variant		ENST00000371847.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA6	ENST00000371847.8	c.1194+1048G>A		intron_variant		1	NM_019073.4	P4

Frequencies

GnomAD3 genomes AF: 0.426 AC: 64707 AN: 151746 Hom.: 14909 Cov.: 32

Gnomad AFR AF: 0.617

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.415

Gnomad ASJ AF: 0.303

Gnomad EAS AF: 0.214

Gnomad SAS AF: 0.411

Gnomad FIN AF: 0.348

Gnomad MID AF: 0.408

Gnomad NFE AF: 0.351

Gnomad OTH AF: 0.397

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

GnomAD4 genome AF: 0.427 AC: 64771 AN: 151866 Hom.: 14931 Cov.: 32 AF XY: 0.423 AC XY: 31368 AN XY: 74188

Gnomad4 AFR AF: 0.617

Gnomad4 AMR AF: 0.414

Gnomad4 ASJ AF: 0.303

Gnomad4 EAS AF: 0.214

Gnomad4 SAS AF: 0.412

Gnomad4 FIN AF: 0.348

Gnomad4 NFE AF: 0.351

Gnomad4 OTH AF: 0.395

Alfa AF: 0.364 Hom.: 10373

Bravo AF: 0.438

Asia WGS AF: 0.311 AC: 1086 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
Cadd	Benign	5.9
Dann	Benign	0.64

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: rs11205476; hg19: chr1-48820294; COSMIC: COSV64056752; COSMIC: COSV64056752;