rs187283

chr16-89662928-A-Gchr16-89662928-A-T

Variant summary

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

The NM_001271907.2(SPATA33):c.211+4507A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.748 in 151,606 control chromosomes in the GnomAD database, including 44,023 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 0.75 (44023 hom., cov: 30)
• Consequence: SPATA33 NM_001271907.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.67

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=-1.01).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.81 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA33	NM_001271907.2	c.211+4507A>G		intron_variant		ENST00000579310.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA33	ENST00000579310.6	c.211+4507A>G		intron_variant		2	NM_001271907.2	P2

Frequencies

GnomAD3 genomes AF: 0.748 AC: 113304 AN: 151488 Hom.: 43995 Cov.: 30

Gnomad AFR AF: 0.766

Gnomad AMI AF: 0.923

Gnomad AMR AF: 0.626

Gnomad ASJ AF: 0.857

Gnomad EAS AF: 0.0948

Gnomad SAS AF: 0.755

Gnomad FIN AF: 0.672

Gnomad MID AF: 0.854

Gnomad NFE AF: 0.816

Gnomad OTH AF: 0.777

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

GnomAD4 genome AF: 0.748 AC: 113378 AN: 151606 Hom.: 44023 Cov.: 30 AF XY: 0.736 AC XY: 54475 AN XY: 74050

Gnomad4 AFR AF: 0.766

Gnomad4 AMR AF: 0.625

Gnomad4 ASJ AF: 0.857

Gnomad4 EAS AF: 0.0946

Gnomad4 SAS AF: 0.755

Gnomad4 FIN AF: 0.672

Gnomad4 NFE AF: 0.816

Gnomad4 OTH AF: 0.773

Alfa AF: 0.849 Hom.: 9235

Bravo AF: 0.736

Asia WGS AF: 0.432 AC: 1503 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
Cadd	Benign	1.6
Dann	Benign	0.22

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: rs187283; hg19: chr16-89729336;