dbSNP rs632376: SPATA2:c.*1546T>C (chr20-49904073-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The NM_006038.4(SPATA2):c.*1546T>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 0.337 in 151,962 control chromosomes in the GnomAD database, including 10,870 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 0.34 ( 10804 hom., cov: 29)

Exomes 𝑓: 0.57 ( 66 hom. )

Consequence

SPATA2
NM_006038.4 3_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.522

Publications

13 publications found

Variant links:

Genes affected

SPATA2 (HGNC:14681): (spermatogenesis associated 2) Enables signaling receptor complex adaptor activity and ubiquitin-specific protease binding activity. Involved in several processes, including protein deubiquitination; regulation of necroptotic process; and regulation of tumor necrosis factor-mediated signaling pathway. Located in cytoplasm; fibrillar center; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]

SPATA2 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=-0.74).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.541 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006038.4. 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
	SPATA2	NM_006038.4	MANE Select	c.*1546T>C		3_prime_UTR	Exon 3 of 3	NP_006029.1	Q9UM82
	SPATA2	NM_001135773.2		c.*1546T>C		3_prime_UTR	Exon 3 of 3	NP_001129245.1	Q9UM82

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	SPATA2	ENST00000289431.10	TSL:1 MANE Select	c.*1546T>C		3_prime_UTR	Exon 3 of 3	ENSP00000289431.5	Q9UM82
	SPATA2	ENST00000422556.1	TSL:2	c.*1546T>C		3_prime_UTR	Exon 3 of 3	ENSP00000416799.1	Q9UM82

Frequencies

GnomAD3 genomes

AF:

0.337

AC:

50965

AN:

151424

Hom.:

10792

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0776

Gnomad AMI

AF:

0.316

Gnomad AMR

AF:

0.435

Gnomad ASJ

AF:

0.324

Gnomad EAS

AF:

0.343

Gnomad SAS

AF:

0.557

Gnomad FIN

AF:

0.564

Gnomad MID

AF:

0.307

Gnomad NFE

AF:

0.422

Gnomad OTH

AF:

0.343

GnomAD4 exome

AF:

0.574

AC:

241

AN:

420

Hom.:

Cov.:

AF XY:

0.587

AC XY:

149

AN XY:

254

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AC:

AN:

European-Finnish (FIN)

AF:

0.580

AC:

240

AN:

414

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.00

AC:

AN:

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.507

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

GnomAD4 genome

AF:

0.336

AC:

50986

AN:

151542

Hom.:

10804

Cov.:

AF XY:

0.351

AC XY:

25959

AN XY:

74016

show subpopulations

African (AFR)

AF:

0.0774

AC:

3200

AN:

41354

American (AMR)

AF:

0.436

AC:

6611

AN:

15174

Ashkenazi Jewish (ASJ)

AF:

0.324

AC:

1124

AN:

3468

East Asian (EAS)

AF:

0.344

AC:

1775

AN:

5156

South Asian (SAS)

AF:

0.558

AC:

2689

AN:

4818

European-Finnish (FIN)

AF:

0.564

AC:

5899

AN:

10454

Middle Eastern (MID)

AF:

0.313

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.422

AC:

28586

AN:

67810

Other (OTH)

AF:

0.343

AC:

723

AN:

2106

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.536

Heterozygous variant carriers

1439

2878

4317

5756

7195

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

498

996

1494

1992

2490

<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:

0.348

Hom.:

2625

Bravo

AF:

0.308

Asia WGS

AF:

0.453

AC:

1577

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

6.0

(source)

DANN

Benign

0.84

PhyloP100

0.52

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

ClinVar

Computational scores

Splicing

Publications

Other links and lift over