chr16-89667941-T-C

Position:

• chr16-89667941-T-C

Variant summary

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

The NM_001271907.2(SPATA33):​c.212-1345T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.328 in 152,204 control chromosomes in the GnomAD database, including 10,126 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 0.33 (10113 hom., cov: 33)
  • Exomes 𝑓: 0.46 (13 hom.)
• Consequence: SPATA33 NM_001271907.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.295

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]

SPATA33 (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.443 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA33	NM_001271907.2	c.212-1345T>C		intron_variant		ENST00000579310.6	NP_001258836.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA33	ENST00000579310.6	c.212-1345T>C		intron_variant		2	NM_001271907.2	ENSP00000462996.1

Frequencies

GnomAD3 genomes AF: 0.328 AC: 49849 AN: 151990 Hom.: 10112 Cov.: 33

Gnomad AFR AF: 0.125

Gnomad AMI AF: 0.631

Gnomad AMR AF: 0.367

Gnomad ASJ AF: 0.547

Gnomad EAS AF: 0.0206

Gnomad SAS AF: 0.228

Gnomad FIN AF: 0.375

Gnomad MID AF: 0.617

Gnomad NFE AF: 0.447

Gnomad OTH AF: 0.412

GnomAD4 exome AF: 0.458 AC: 44 AN: 96 Hom.: 13 AF XY: 0.500 AC XY: 37 AN XY: 74

Gnomad4 AFR exome AF: 0.250

Gnomad4 EAS exome AF: 0.00

Gnomad4 FIN exome AF: 0.00

Gnomad4 NFE exome AF: 0.512

GnomAD4 genome AF: 0.328 AC: 49852 AN: 152108 Hom.: 10113 Cov.: 33 AF XY: 0.322 AC XY: 23964 AN XY: 74332

Gnomad4 AFR AF: 0.125

Gnomad4 AMR AF: 0.366

Gnomad4 ASJ AF: 0.547

Gnomad4 EAS AF: 0.0205

Gnomad4 SAS AF: 0.229

Gnomad4 FIN AF: 0.375

Gnomad4 NFE AF: 0.447

Gnomad4 OTH AF: 0.408

Alfa AF: 0.411 Hom.: 7037

Bravo AF: 0.320

Asia WGS AF: 0.143 AC: 497 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	3.1
DANN	Benign	0.55

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: rs447735; hg19: chr16-89734349;