2-200477638-T-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001100423.2(SPATS2L):āc.1284T>Gā(p.Asn428Lys) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000694 in 1,541,244 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 (ā ).
Frequency
Genomes: š 0.00041 ( 0 hom., cov: 32)
Exomes š: 0.000032 ( 0 hom. )
Consequence
SPATS2L
NM_001100423.2 missense, splice_region
NM_001100423.2 missense, splice_region
Scores
1
5
13
Clinical Significance
Conservation
PhyloP100: 0.638
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 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SPATS2L | NM_001100423.2 | c.1284T>G | p.Asn428Lys | missense_variant, splice_region_variant | 13/13 | ENST00000409140.8 | NP_001093893.1 | |
LOC101927741 | XR_007088047.1 | n.336A>C | non_coding_transcript_exon_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SPATS2L | ENST00000409140.8 | c.1284T>G | p.Asn428Lys | missense_variant, splice_region_variant | 13/13 | 2 | NM_001100423.2 | ENSP00000386730 | P1 | |
ENST00000655656.1 | n.333A>C | non_coding_transcript_exon_variant | 1/5 |
Frequencies
GnomAD3 genomes AF: 0.000408 AC: 62AN: 151802Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000506 AC: 8AN: 158090Hom.: 0 AF XY: 0.0000357 AC XY: 3AN XY: 83932
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GnomAD4 exome AF: 0.0000324 AC: 45AN: 1389326Hom.: 0 Cov.: 32 AF XY: 0.0000175 AC XY: 12AN XY: 684336
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GnomAD4 genome AF: 0.000408 AC: 62AN: 151918Hom.: 0 Cov.: 32 AF XY: 0.000391 AC XY: 29AN XY: 74250
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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 | Nov 30, 2022 | The c.1284T>G (p.N428K) alteration is located in exon 13 (coding exon 11) of the SPATS2L gene. This alteration results from a T to G substitution at nucleotide position 1284, causing the asparagine (N) at amino acid position 428 to be replaced by a lysine (K). 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
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Uncertain
DEOGEN2
Benign
T;T;T;T;T;.;T;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;.;D;.;D;D;D;D
M_CAP
Benign
T
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
Benign
T;T;T;T;T;T;T;T;.
Polyphen
P;P;P;.;P;P;P;.;.
Vest4
MutPred
Gain of methylation at N428 (P = 0.0098);Gain of methylation at N428 (P = 0.0098);Gain of methylation at N428 (P = 0.0098);.;Gain of methylation at N428 (P = 0.0098);.;Gain of methylation at N428 (P = 0.0098);.;.;
MVP
MPC
0.44
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_AG_spliceai
Position offset: 1
Find out detailed SpliceAI scores and Pangolin per-transcript scores at