Variant chr16-89657860-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_001271907.2(SPATA33):c.-52C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0978 in 1,509,182 control chromosomes in the GnomAD database, including 8,154 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.075 ( 557 hom., cov: 32)

Exomes 𝑓: 0.10 ( 7597 hom. )

Consequence

SPATA33
NM_001271907.2 5_prime_UTR

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.35

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:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.0017423034).

BP6

Variant 16-89657860-C-T is Benign according to our data. Variant chr16-89657860-C-T is described in ClinVar as [Benign]. Clinvar id is 1183917.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.119 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
SPATA33	NM_001271907.2 linkuse as main transcript	c.-52C>T		5_prime_UTR_variant	1/3	ENST00000579310.6

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
SPATA33	ENST00000579310.6 linkuse as main transcript	c.-52C>T		5_prime_UTR_variant	1/3	2	NM_001271907.2	P2	Q96N06-2

Frequencies

GnomAD3 genomes

AF:

0.0751

AC:

11397

AN:

151850

Hom.:

557

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0245

Gnomad AMI

AF:

0.0471

Gnomad AMR

AF:

0.123

Gnomad ASJ

AF:

0.0759

Gnomad EAS

AF:

0.128

Gnomad SAS

AF:

0.0797

Gnomad FIN

AF:

0.120

Gnomad MID

AF:

0.00955

Gnomad NFE

AF:

0.0850

Gnomad OTH

AF:

0.0561

GnomAD3 exomes

AF:

0.101

AC:

10252

AN:

101962

Hom.:

653

AF XY:

0.0964

AC XY:

5526

AN XY:

57352

show subpopulations

Gnomad AFR exome

AF:

0.0235

Gnomad AMR exome

AF:

0.157

Gnomad ASJ exome

AF:

0.0711

Gnomad EAS exome

AF:

0.130

Gnomad SAS exome

AF:

0.0700

Gnomad FIN exome

AF:

0.129

Gnomad NFE exome

AF:

0.0884

Gnomad OTH exome

AF:

0.0706

GnomAD4 exome

AF:

0.100

AC:

136194

AN:

1357222

Hom.:

7597

Cov.:

AF XY:

0.0986

AC XY:

66030

AN XY:

669728

show subpopulations

Gnomad4 AFR exome

AF:

0.0190

Gnomad4 AMR exome

AF:

0.151

Gnomad4 ASJ exome

AF:

0.0724

Gnomad4 EAS exome

AF:

0.150

Gnomad4 SAS exome

AF:

0.0694

Gnomad4 FIN exome

AF:

0.120

Gnomad4 NFE exome

AF:

0.102

Gnomad4 OTH exome

AF:

0.0923

GnomAD4 genome

AF:

0.0750

AC:

11400

AN:

151960

Hom.:

557

Cov.:

AF XY:

0.0778

AC XY:

5781

AN XY:

74288

show subpopulations

Gnomad4 AFR

AF:

0.0244

Gnomad4 AMR

AF:

0.123

Gnomad4 ASJ

AF:

0.0759

Gnomad4 EAS

AF:

0.127

Gnomad4 SAS

AF:

0.0794

Gnomad4 FIN

AF:

0.120

Gnomad4 NFE

AF:

0.0850

Gnomad4 OTH

AF:

0.0598

Alfa

AF:

0.0503

Hom.:

Bravo

AF:

0.0741

TwinsUK

AF:

0.112

AC:

416

ALSPAC

AF:

0.101

AC:

390

ESP6500AA

AF:

0.0142

AC:

ESP6500EA

AF:

0.0504

AC:

195

ExAC

AF:

0.0403

AC:

839

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jun 26, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.57

BayesDel_noAF

Benign

-0.45

CADD

Benign

4.2

DANN

Benign

0.95

FATHMM_MKL

Benign

0.065

LIST_S2

Benign

0.33

MetaRNN

Benign

0.0017

MutationTaster

Benign

0.97

P;P

Sift4G

Uncertain

0.0050

GERP RS

-0.65

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over