chr2-200477657-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001100423.2(SPATS2L):c.1303C>T(p.Arg435Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00002 in 1,551,668 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.000020 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000020 ( 0 hom. )
Consequence
SPATS2L
NM_001100423.2 missense
NM_001100423.2 missense
Scores
4
6
8
Clinical Significance
Conservation
PhyloP100: 3.30
Genes affected
SPATS2L (HGNC:24574): (spermatogenesis associated serine rich 2 like) Enables RNA binding activity. Located in cytosol; nucleolus; and nucleoplasm. Part of protein-containing complex. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 1 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (MetaRNN=0.3097055).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATS2L | NM_001100423.2 | c.1303C>T | p.Arg435Trp | missense_variant | 13/13 | ENST00000409140.8 | |
LOC101927741 | XR_007088047.1 | n.317G>A | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATS2L | ENST00000409140.8 | c.1303C>T | p.Arg435Trp | missense_variant | 13/13 | 2 | NM_001100423.2 | P1 | |
ENST00000655656.1 | n.314G>A | non_coding_transcript_exon_variant | 1/5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000198 AC: 3AN: 151888Hom.: 0 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.0000200 AC: 28AN: 1399664Hom.: 0 Cov.: 32 AF XY: 0.0000232 AC XY: 16AN XY: 690766
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GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152004Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74286
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Asia WGS
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AN:
3478
ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 16, 2023 | The c.1303C>T (p.R435W) alteration is located in exon 13 (coding exon 11) of the SPATS2L gene. This alteration results from a C to T substitution at nucleotide position 1303, causing the arginine (R) at amino acid position 435 to be replaced by a tryptophan (W). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Benign
T;T;T;T;T;.;T;.;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
M_CAP
Benign
D
MetaRNN
Benign
T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
L;L;L;.;L;.;L;.;.
MutationTaster
Benign
D;D;D;D;D;D;D;D;D
PrimateAI
Uncertain
T
PROVEAN
Benign
N;N;N;N;N;N;N;.;N
REVEL
Benign
Sift
Uncertain
D;D;D;D;D;D;D;.;D
Sift4G
Uncertain
D;D;D;D;D;D;D;D;.
Polyphen
D;D;D;.;D;D;D;.;.
Vest4
MutPred
Gain of loop (P = 0.0435);Gain of loop (P = 0.0435);Gain of loop (P = 0.0435);.;Gain of loop (P = 0.0435);.;Gain of loop (P = 0.0435);.;.;
MVP
MPC
0.83
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at