rs2485911

Positions:

• chr1-48445304-G-A

Variant summary

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

The NM_019073.4(SPATA6):​c.238+6248C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.4 in 151,994 control chromosomes in the GnomAD database, including 12,847 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 0.40 (12847 hom., cov: 32)
• Consequence: SPATA6 NM_019073.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.711

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=-0.86).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.54 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA6	NM_019073.4	c.238+6248C>T		intron_variant		ENST00000371847.8	NP_061946.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA6	ENST00000371847.8	c.238+6248C>T		intron_variant		1	NM_019073.4	ENSP00000360913	P4

Frequencies

GnomAD3 genomes AF: 0.400 AC: 60727 AN: 151878 Hom.: 12828 Cov.: 32

Gnomad AFR AF: 0.546

Gnomad AMI AF: 0.344

Gnomad AMR AF: 0.404

Gnomad ASJ AF: 0.302

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.360

Gnomad FIN AF: 0.317

Gnomad MID AF: 0.396

Gnomad NFE AF: 0.349

Gnomad OTH AF: 0.375

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

GnomAD4 genome AF: 0.400 AC: 60782 AN: 151994 Hom.: 12847 Cov.: 32 AF XY: 0.395 AC XY: 29326 AN XY: 74296

Gnomad4 AFR AF: 0.546

Gnomad4 AMR AF: 0.404

Gnomad4 ASJ AF: 0.302

Gnomad4 EAS AF: 0.187

Gnomad4 SAS AF: 0.361

Gnomad4 FIN AF: 0.317

Gnomad4 NFE AF: 0.349

Gnomad4 OTH AF: 0.373

Alfa AF: 0.382 Hom.: 1995

Bravo AF: 0.411

Asia WGS AF: 0.278 AC: 970 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.86
CADD	Benign	4.5
DANN	Benign	0.37

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: rs2485911; hg19: chr1-48910976; COSMIC: COSV64060496; COSMIC: COSV64060496;