16-89660076-G-T

Variant names:

• chr16-89660076-G-T
• rs7188458
• ENST00000564238.2:c.*1772G>T

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000564238.2(SPATA33):​c.*1772G>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 33)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• Consequence: SPATA33 ENST00000564238.2 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.310
• Publications: 34 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.92).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000564238.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA33	NM_001271907.2	MANE Select	c.211+1655G>T		intron	N/A	NP_001258836.1	Q96N06-2
	SPATA33	NM_001387226.1		c.241+1625G>T		intron	N/A	NP_001374155.1
	SPATA33	NM_153025.3		c.208+1655G>T		intron	N/A	NP_694570.1	Q96N06-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA33	ENST00000564238.2	TSL:1	c.*1772G>T		3_prime_UTR	Exon 2 of 2	ENSP00000462233.2	J3KS00
	SPATA33	ENST00000579310.6	TSL:2 MANE Select	c.211+1655G>T		intron	N/A	ENSP00000462996.1	Q96N06-2
	SPATA33	ENST00000301031.8	TSL:1	c.208+1655G>T		intron	N/A	ENSP00000301031.4	Q96N06-1

Frequencies

GnomAD3 genomes Cov.: 33

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 5270 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2666

African (AFR) AF: 0.00 AC: 0 AN: 242

American (AMR) AF: 0.00 AC: 0 AN: 132

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 218

East Asian (EAS) AF: 0.00 AC: 0 AN: 258

South Asian (SAS) AF: 0.00 AC: 0 AN: 52

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 250

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 20

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 3724

Other (OTH) AF: 0.00 AC: 0 AN: 374

GnomAD4 genome Cov.: 33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.6
DANN	Benign	0.57
PhyloP100		-0.31

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: rs7188458; hg19: chr16-89726484;