rs11205476

Variant names:

• chr1-48354622-C-T
• rs11205476
• NM_019073.4:c.1194+1048G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SPATA6	NM_019073.4	c.1194+1048G>A		intron_variant	Intron 11 of 12	ENST00000371847.8	NP_061946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA6	ENST00000371847.8	c.1194+1048G>A		intron_variant	Intron 11 of 12	1	NM_019073.4	ENSP00000360913.3

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

African (AFR) AF: 0.617 AC: 25587 AN: 41458

American (AMR) AF: 0.414 AC: 6314 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.303 AC: 1048 AN: 3462

East Asian (EAS) AF: 0.214 AC: 1101 AN: 5156

South Asian (SAS) AF: 0.412 AC: 1983 AN: 4812

European-Finnish (FIN) AF: 0.348 AC: 3668 AN: 10546

Middle Eastern (MID) AF: 0.394 AC: 115 AN: 292

European-Non Finnish (NFE) AF: 0.351 AC: 23813 AN: 67896

Other (OTH) AF: 0.395 AC: 829 AN: 2100

Alfa AF: 0.374 Hom.: 14339

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
PhyloP100		-0.20
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

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