rs2377058

Positions:

• chr16-89668423-A-G

Variant summary

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

The NM_001271907.2(SPATA33):​c.212-863A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.378 in 152,152 control chromosomes in the GnomAD database, including 11,841 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 0.38 (11841 hom., cov: 34)
• Consequence: SPATA33 NM_001271907.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.00600

Genes affected

SPATA33 (HGNC:26463): (spermatogenesis associated 33) Predicted to act upstream of or within cellular protein localization; fertilization; and flagellated sperm motility. Predicted to be located in sperm mitochondrial sheath. Predicted to be active in cytoplasm and nucleus. [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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA33	NM_001271907.2	c.212-863A>G		intron_variant		ENST00000579310.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA33	ENST00000579310.6	c.212-863A>G		intron_variant		2	NM_001271907.2	P2

Frequencies

GnomAD3 genomes AF: 0.378 AC: 57396 AN: 152034 Hom.: 11828 Cov.: 34

Gnomad AFR AF: 0.524

Gnomad AMI AF: 0.267

Gnomad AMR AF: 0.241

Gnomad ASJ AF: 0.306

Gnomad EAS AF: 0.0750

Gnomad SAS AF: 0.523

Gnomad FIN AF: 0.274

Gnomad MID AF: 0.228

Gnomad NFE AF: 0.356

Gnomad OTH AF: 0.331

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

GnomAD4 genome AF: 0.378 AC: 57448 AN: 152152 Hom.: 11841 Cov.: 34 AF XY: 0.372 AC XY: 27648 AN XY: 74396

Gnomad4 AFR AF: 0.523

Gnomad4 AMR AF: 0.241

Gnomad4 ASJ AF: 0.306

Gnomad4 EAS AF: 0.0750

Gnomad4 SAS AF: 0.522

Gnomad4 FIN AF: 0.274

Gnomad4 NFE AF: 0.355

Gnomad4 OTH AF: 0.332

Alfa AF: 0.351 Hom.: 15036

Bravo AF: 0.371

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.58

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: rs2377058; hg19: chr16-89734831;