Genetic Variant SPATA33:c.*1323T>C (chr16-89659627-T-C) – 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.*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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.721

Publications

6 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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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=-1.03).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.899 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+1206T>C	intron	N/A	NP_001258836.1	Q96N06-2
SPATA33	NM_001387226.1		c.241+1176T>C	intron	N/A	NP_001374155.1
SPATA33	NM_153025.3		c.208+1206T>C	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.*1323T>C	3_prime_UTR	Exon 2 of 2	ENSP00000462233.2	J3KS00
SPATA33	ENST00000579310.6	TSL:2 MANE Select	c.211+1206T>C	intron	N/A	ENSP00000462996.1	Q96N06-2
SPATA33	ENST00000301031.8	TSL:1	c.208+1206T>C	intron	N/A	ENSP00000301031.4	Q96N06-1

Frequencies

GnomAD3 genomes

AF:

0.854

AC:

129673

AN:

151824

Hom.:

55672

Cov.:

show subpopulations

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:

AN:

104

Hom.:

Cov.:

AF XY:

0.897

AC XY:

AN XY:

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AF:

1.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.750

AC:

AN:

Middle Eastern (MID)

AF:

1.00

AC:

AN:

European-Non Finnish (NFE)

AF:

0.905

AC:

AN:

Other (OTH)

AF:

0.750

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.520

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

<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:

0.854

AC:

129763

AN:

151942

Hom.:

55711

Cov.:

AF XY:

0.848

AC XY:

62954

AN XY:

74236

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

930

1860

2790

3720

4650

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

888

1776

2664

3552

4440

<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:

0.865

Hom.:

21855

Bravo

AF:

0.842

Asia WGS

AF:

0.770

AC:

2678

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.0

(source)

DANN

Benign

0.33

PhyloP100

-0.72

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

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