rs7188458

Positions:

• chr16-89660076-G-A
• chr16-89660076-G-T

Variant summary

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

The ENST00000564238.2(SPATA33):​c.*1772G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 157,330 control chromosomes in the GnomAD database, including 16,139 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 0.45 (15693 hom., cov: 33)
  • Exomes 𝑓: 0.41 (446 hom.)
• Consequence: SPATA33 ENST00000564238.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310

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=-0.95).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.579 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA33	NM_001271907.2	c.211+1655G>A		intron_variant		ENST00000579310.6	NP_001258836.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA33	ENST00000579310.6	c.211+1655G>A		intron_variant		2	NM_001271907.2	ENSP00000462996.1

Frequencies

GnomAD3 genomes AF: 0.447 AC: 67934 AN: 151962 Hom.: 15684 Cov.: 33

Gnomad AFR AF: 0.537

Gnomad AMI AF: 0.305

Gnomad AMR AF: 0.361

Gnomad ASJ AF: 0.382

Gnomad EAS AF: 0.187

Gnomad SAS AF: 0.598

Gnomad FIN AF: 0.376

Gnomad MID AF: 0.222

Gnomad NFE AF: 0.440

Gnomad OTH AF: 0.381

GnomAD4 exome AF: 0.409 AC: 2146 AN: 5248 Hom.: 446 Cov.: 0 AF XY: 0.407 AC XY: 1081 AN XY: 2656

Gnomad4 AFR exome AF: 0.579

Gnomad4 AMR exome AF: 0.356

Gnomad4 ASJ exome AF: 0.399

Gnomad4 EAS exome AF: 0.236

Gnomad4 SAS exome AF: 0.519

Gnomad4 FIN exome AF: 0.323

Gnomad4 NFE exome AF: 0.421

Gnomad4 OTH exome AF: 0.377

GnomAD4 genome AF: 0.447 AC: 67974 AN: 152082 Hom.: 15693 Cov.: 33 AF XY: 0.444 AC XY: 32991 AN XY: 74368

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.360

Gnomad4 ASJ AF: 0.382

Gnomad4 EAS AF: 0.186

Gnomad4 SAS AF: 0.597

Gnomad4 FIN AF: 0.376

Gnomad4 NFE AF: 0.440

Gnomad4 OTH AF: 0.386

Alfa AF: 0.428 Hom.: 19790

Bravo AF: 0.439

Asia WGS AF: 0.389 AC: 1352 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	2.9
DANN	Benign	0.61

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: rs7188458; hg19: chr16-89726484;