chr2-200440744-G-A
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Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_001100423.2(SPATS2L):c.748G>A(p.Val250Met) variant causes a missense change. The variant allele was found at a frequency of 0.0000124 in 1,613,620 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: 0.000012 ( 0 hom. )
Consequence
SPATS2L
NM_001100423.2 missense
NM_001100423.2 missense
Scores
4
7
8
Clinical Significance
Conservation
PhyloP100: 4.48
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=0.39907706).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPATS2L | NM_001100423.2 | c.748G>A | p.Val250Met | missense_variant | 8/13 | ENST00000409140.8 | |
LOC101927741 | XR_007088047.1 | n.662+8632C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPATS2L | ENST00000409140.8 | c.748G>A | p.Val250Met | missense_variant | 8/13 | 2 | NM_001100423.2 | P1 | |
ENST00000655656.1 | n.567-9207C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152188Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000281 AC: 7AN: 248776Hom.: 0 AF XY: 0.0000445 AC XY: 6AN XY: 134938
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GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461314Hom.: 0 Cov.: 30 AF XY: 0.0000151 AC XY: 11AN XY: 726914
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GnomAD4 genome AF: 0.0000197 AC: 3AN: 152306Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74466
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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 | Aug 30, 2021 | The c.748G>A (p.V250M) alteration is located in exon 8 (coding exon 6) of the SPATS2L gene. This alteration results from a G to A substitution at nucleotide position 748, causing the valine (V) at amino acid position 250 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Pathogenic
DANN
Pathogenic
DEOGEN2
Benign
T;T;T;T;T;.;T;T;T;.;.;.
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
.;.;.;D;.;D;D;D;D;D;D;D
M_CAP
Benign
T
MetaRNN
Benign
T;T;T;T;T;T;T;T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;M;M;.;M;.;.;M;.;.;.;.
MutationTaster
Benign
D;D;D;D;D;D;D;D;D
PrimateAI
Pathogenic
T
PROVEAN
Benign
N;N;N;N;N;N;N;N;N;.;N;N
REVEL
Uncertain
Sift
Uncertain
D;D;D;D;D;D;D;D;D;.;D;D
Sift4G
Uncertain
D;D;D;D;D;D;D;D;D;D;.;D
Polyphen
D;D;D;.;D;D;.;D;.;.;.;.
Vest4
MutPred
Gain of catalytic residue at V246 (P = 0.0201);Gain of catalytic residue at V246 (P = 0.0201);Gain of catalytic residue at V246 (P = 0.0201);.;Gain of catalytic residue at V246 (P = 0.0201);.;.;Gain of catalytic residue at V246 (P = 0.0201);.;.;.;.;
MVP
MPC
0.85
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at