rs2377058

Variant names:

• chr16-89668423-A-G
• rs2377058
• NM_001271907.2:c.212-863A>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.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
• Publications: 18 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=-0.9).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.518 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001271907.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA33	NM_001271907.2	MANE Select	c.212-863A>G		intron	N/A	NP_001258836.1
	SPATA33	NM_001387226.1		c.242-863A>G		intron	N/A	NP_001374155.1
	SPATA33	NM_153025.3		c.209-863A>G		intron	N/A	NP_694570.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA33	ENST00000579310.6	TSL:2 MANE Select	c.212-863A>G		intron	N/A	ENSP00000462996.1
	SPATA33	ENST00000301031.8	TSL:1	c.209-863A>G		intron	N/A	ENSP00000301031.4
	SPATA33	ENST00000566204.2	TSL:4	c.119-863A>G		intron	N/A	ENSP00000461933.2

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

African (AFR) AF: 0.523 AC: 21730 AN: 41516

American (AMR) AF: 0.241 AC: 3678 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 1061 AN: 3466

East Asian (EAS) AF: 0.0750 AC: 389 AN: 5186

South Asian (SAS) AF: 0.522 AC: 2518 AN: 4828

European-Finnish (FIN) AF: 0.274 AC: 2894 AN: 10580

Middle Eastern (MID) AF: 0.231 AC: 68 AN: 294

European-Non Finnish (NFE) AF: 0.355 AC: 24167 AN: 67984

Other (OTH) AF: 0.332 AC: 701 AN: 2110

Alfa AF: 0.358 Hom.: 36744

Bravo AF: 0.371

Asia WGS AF: 0.279 AC: 971 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	1.0
DANN	Benign	0.58
PhyloP100		0.0060
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: rs2377058; hg19: chr16-89734831;