2-231000413-C-G

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_139073.5(SPATA3):​c.349C>G​(p.Pro117Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000503 in 1,390,410 control chromosomes in the GnomAD database, including 1 homozygotes. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P117S) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 33)
Exomes š‘“: 0.0000050 ( 1 hom. )

Consequence

SPATA3
NM_139073.5 missense

Scores

1
7
11

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 3.03
Variant links:
Genes affected
SPATA3 (HGNC:17884): (spermatogenesis associated 3) Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
SPATA3NM_139073.5 linkc.349C>G p.Pro117Ala missense_variant Exon 2 of 5 ENST00000433428.7 NP_620712.2 Q8NHX4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
SPATA3ENST00000433428.7 linkc.349C>G p.Pro117Ala missense_variant Exon 2 of 5 1 NM_139073.5 ENSP00000403804.2 Q8NHX4

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
AF:
0.00000503
AC:
7
AN:
1390410
Hom.:
1
Cov.:
36
AF XY:
0.00000730
AC XY:
5
AN XY:
684712
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.000198
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.32
BayesDel_addAF
Uncertain
0.16
D
BayesDel_noAF
Uncertain
-0.010
CADD
Uncertain
24
DANN
Benign
0.79
DEOGEN2
Benign
0.034
.;T;T;T;.;T
Eigen
Uncertain
0.35
Eigen_PC
Uncertain
0.28
FATHMM_MKL
Benign
0.71
D
LIST_S2
Benign
0.79
T;.;.;.;T;T
M_CAP
Benign
0.0073
T
MetaRNN
Uncertain
0.58
D;D;D;D;D;D
MetaSVM
Benign
-0.56
T
MutationAssessor
Benign
1.0
.;L;L;L;.;L
PrimateAI
Uncertain
0.52
T
PROVEAN
Uncertain
-4.3
.;D;D;D;.;D
REVEL
Benign
0.26
Sift
Benign
0.065
.;T;T;T;.;T
Sift4G
Pathogenic
0.0
.;D;D;D;D;D
Vest4
0.66, 0.69
MVP
0.12
ClinPred
0.98
D
GERP RS
4.3
Varity_R
0.12
gMVP
0.016

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

No publications associated with this variant yet.

Other links and lift over

hg19: chr2-231865128; API