chr17-50552097-A-T

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_022827.4(SPATA20):​c.1874A>T​(p.Lys625Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

SPATA20
NM_022827.4 missense

Scores

6
13

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.325
Variant links:
Genes affected
SPATA20 (HGNC:26125): (spermatogenesis associated 20) Predicted to be involved in carbohydrate metabolic process; cell differentiation; and spermatogenesis. Predicted to be located in extracellular region. [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 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.22804731).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
SPATA20NM_022827.4 linkuse as main transcriptc.1874A>T p.Lys625Met missense_variant 14/17 ENST00000006658.11 NP_073738.2
SPATA20NM_001258372.2 linkuse as main transcriptc.1826A>T p.Lys609Met missense_variant 13/16 NP_001245301.1
SPATA20NM_001258373.2 linkuse as main transcriptc.1694A>T p.Lys565Met missense_variant 14/17 NP_001245302.1

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
SPATA20ENST00000006658.11 linkuse as main transcriptc.1874A>T p.Lys625Met missense_variant 14/171 NM_022827.4 ENSP00000006658 Q8TB22-2

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
59
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.13
BayesDel_addAF
Benign
-0.16
T
BayesDel_noAF
Benign
-0.47
CADD
Benign
21
DANN
Uncertain
0.99
DEOGEN2
Benign
0.38
.;.;T;T
Eigen
Benign
-0.22
Eigen_PC
Benign
-0.19
FATHMM_MKL
Uncertain
0.82
D
LIST_S2
Benign
0.69
T;T;T;T
M_CAP
Benign
0.029
D
MetaRNN
Benign
0.23
T;T;T;T
MetaSVM
Benign
-0.89
T
MutationAssessor
Uncertain
2.7
.;.;M;.
MutationTaster
Benign
1.0
P;P;P
PrimateAI
Benign
0.32
T
PROVEAN
Uncertain
-2.6
.;D;D;.
REVEL
Benign
0.037
Sift
Uncertain
0.010
.;D;D;.
Sift4G
Uncertain
0.033
D;D;D;D
Polyphen
0.58, 0.15
.;P;B;.
Vest4
0.34
MutPred
0.42
.;.;Loss of ubiquitination at K609 (P = 0.0309);Loss of ubiquitination at K609 (P = 0.0309);
MVP
0.13
MPC
0.53
ClinPred
0.96
D
GERP RS
1.6
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.11
gMVP
0.32

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.13
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.

Other links and lift over

dbSNP: rs8065903; hg19: chr17-48629458; API