16-89662928-A-G

Variant names:

• chr16-89662928-A-G
• rs187283
• NM_001271907.2:c.211+4507A>G

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 5 publications found

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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
SPATA33	NM_001271907.2	c.211+4507A>G		intron_variant	Intron 2 of 2	ENST00000579310.6	NP_001258836.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
SPATA33	ENST00000579310.6	c.211+4507A>G		intron_variant	Intron 2 of 2	2	NM_001271907.2	ENSP00000462996.1

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

African (AFR) AF: 0.766 AC: 31631 AN: 41290

American (AMR) AF: 0.625 AC: 9520 AN: 15234

Ashkenazi Jewish (ASJ) AF: 0.857 AC: 2975 AN: 3472

East Asian (EAS) AF: 0.0946 AC: 484 AN: 5116

South Asian (SAS) AF: 0.755 AC: 3623 AN: 4798

European-Finnish (FIN) AF: 0.672 AC: 7047 AN: 10492

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.816 AC: 55379 AN: 67896

Other (OTH) AF: 0.773 AC: 1624 AN: 2102

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
PhyloP100		-1.7
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: rs187283; hg19: chr16-89729336;