Variant rs632376 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -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

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 made for transcript

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
SPATA2	NM_006038.4 linkuse as main transcript	c.*1546T>C		3_prime_UTR_variant	3/3	ENST00000289431.10	NP_006029.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
SPATA2	ENST00000289431.10 linkuse as main transcript	c.*1546T>C		3_prime_UTR_variant	3/3	1	NM_006038.4	ENSP00000289431	P1
SPATA2	ENST00000422556.1 linkuse as main transcript	c.*1546T>C		3_prime_UTR_variant	3/3	2		ENSP00000416799	P1

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

Gnomad4 FIN exome

AF:

0.580

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.336

AC:

50986

AN:

151542

Hom.:

10804

Cov.:

AF XY:

0.351

AC XY:

25959

AN XY:

74016

show subpopulations

Gnomad4 AFR

AF:

0.0774

Gnomad4 AMR

AF:

0.436

Gnomad4 ASJ

AF:

0.324

Gnomad4 EAS

AF:

0.344

Gnomad4 SAS

AF:

0.558

Gnomad4 FIN

AF:

0.564

Gnomad4 NFE

AF:

0.422

Gnomad4 OTH

AF:

0.343

Alfa

AF:

0.280

Hom.:

880

Bravo

AF:

0.308

Asia WGS

AF:

0.453

AC:

1577

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.74

CADD

Benign

6.0

DANN

Benign

0.84

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over