ENST00000564238.2:c.*1323T>C

Variant names:

• chr16-89659627-T-C
• rs154663
• ENST00000564238.2:c.*1323T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000564238.2(SPATA33):​c.*1323T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.854 in 152,046 control chromosomes in the GnomAD database, including 55,752 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 0.85 (55711 hom., cov: 31)
  • Exomes 𝑓: 0.89 (41 hom.)
• Consequence: SPATA33 ENST00000564238.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.721
• Publications: 6 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=-1.03).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.899 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
SPATA33	NM_001271907.2	c.211+1206T>C		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+1206T>C		intron_variant	Intron 2 of 2	2	NM_001271907.2	ENSP00000462996.1

Frequencies

GnomAD3 genomes AF: 0.854 AC: 129673 AN: 151824 Hom.: 55672 Cov.: 31

Gnomad AFR AF: 0.815

Gnomad AMI AF: 0.970

Gnomad AMR AF: 0.761

Gnomad ASJ AF: 0.937

Gnomad EAS AF: 0.724

Gnomad SAS AF: 0.867

Gnomad FIN AF: 0.829

Gnomad MID AF: 0.870

Gnomad NFE AF: 0.905

Gnomad OTH AF: 0.862

GnomAD4 exome AF: 0.894 AC: 93 AN: 104 Hom.: 41 Cov.: 0 AF XY: 0.897 AC XY: 70 AN XY: 78

African (AFR) AF: 1.00 AC: 2 AN: 2

American (AMR) AF: 1.00 AC: 2 AN: 2

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AF: 1.00 AC: 2 AN: 2

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AF: 0.750 AC: 3 AN: 4

Middle Eastern (MID) AF: 1.00 AC: 2 AN: 2

European-Non Finnish (NFE) AF: 0.905 AC: 76 AN: 84

Other (OTH) AF: 0.750 AC: 6 AN: 8

GnomAD4 genome AF: 0.854 AC: 129763 AN: 151942 Hom.: 55711 Cov.: 31 AF XY: 0.848 AC XY: 62954 AN XY: 74236

African (AFR) AF: 0.815 AC: 33779 AN: 41438

American (AMR) AF: 0.760 AC: 11594 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.937 AC: 3252 AN: 3472

East Asian (EAS) AF: 0.724 AC: 3727 AN: 5146

South Asian (SAS) AF: 0.867 AC: 4175 AN: 4814

European-Finnish (FIN) AF: 0.829 AC: 8741 AN: 10546

Middle Eastern (MID) AF: 0.874 AC: 257 AN: 294

European-Non Finnish (NFE) AF: 0.905 AC: 61535 AN: 67964

Other (OTH) AF: 0.863 AC: 1820 AN: 2110

Alfa AF: 0.865 Hom.: 21855

Bravo AF: 0.842

Asia WGS AF: 0.770 AC: 2678 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	1.0
DANN	Benign	0.33
PhyloP100		-0.72
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: rs154663; hg19: chr16-89726035;