Genetic Variant SPATA33:c.*1772G>A (chr16-89660076-G-A) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.310

Publications

34 publications found

Variant links:

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 links:

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new If you want to explore the variant's impact on the transcript ENST00000564238.2, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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.

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

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

Ensembl Transcripts

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

Frequencies

GnomAD3 genomes

AF:

0.447

AC:

67934

AN:

151962

Hom.:

15684

Cov.:

show subpopulations

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.:

AF XY:

0.407

AC XY:

1081

AN XY:

2656

show subpopulations

African (AFR)

AF:

0.579

AC:

139

AN:

240

American (AMR)

AF:

0.356

AC:

AN:

132

Ashkenazi Jewish (ASJ)

AF:

0.399

AC:

AN:

218

East Asian (EAS)

AF:

0.236

AC:

AN:

258

South Asian (SAS)

AF:

0.519

AC:

AN:

European-Finnish (FIN)

AF:

0.323

AC:

AN:

248

Middle Eastern (MID)

AF:

0.200

AC:

AN:

European-Non Finnish (NFE)

AF:

0.421

AC:

1560

AN:

3706

Other (OTH)

AF:

0.377

AC:

141

AN:

374

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

133

200

266

333

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

100

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.447

AC:

67974

AN:

152082

Hom.:

15693

Cov.:

AF XY:

0.444

AC XY:

32991

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.536

AC:

22232

AN:

41452

American (AMR)

AF:

0.360

AC:

5504

AN:

15286

Ashkenazi Jewish (ASJ)

AF:

0.382

AC:

1325

AN:

3472

East Asian (EAS)

AF:

0.186

AC:

967

AN:

5190

South Asian (SAS)

AF:

0.597

AC:

2883

AN:

4830

European-Finnish (FIN)

AF:

0.376

AC:

3979

AN:

10576

Middle Eastern (MID)

AF:

0.228

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.440

AC:

29926

AN:

67964

Other (OTH)

AF:

0.386

AC:

813

AN:

2108

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

1926

3852

5778

7704

9630

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

634

1268

1902

2536

3170

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.430

Hom.:

25171

Bravo

AF:

0.439

Asia WGS

AF:

0.389

AC:

1352

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.9

(source)

DANN

Benign

0.61

PhyloP100

-0.31

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over