5-169588454-T-G
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017785.5(SPDL1):āc.38T>Gā(p.Leu13Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0000514 in 1,613,276 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Genomes: š 0.000046 ( 0 hom., cov: 32)
Exomes š: 0.000052 ( 0 hom. )
Consequence
SPDL1
NM_017785.5 missense
NM_017785.5 missense
Scores
5
12
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 6.53
Genes affected
SPDL1 (HGNC:26010): (spindle apparatus coiled-coil protein 1) This gene encodes a coiled-coil domain-containing protein that functions in mitotic spindle formation and chromosome segregation. The encoded protein plays a role in coordinating microtubule attachment by promoting recruitment of dynein proteins, and in mitotic checkpoint signaling. [provided by RefSeq, Jul 2016]
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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 | UniProt |
---|---|---|---|---|---|---|---|
SPDL1 | NM_017785.5 | c.38T>G | p.Leu13Arg | missense_variant | 2/12 | ENST00000265295.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPDL1 | ENST00000265295.9 | c.38T>G | p.Leu13Arg | missense_variant | 2/12 | 1 | NM_017785.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000460 AC: 7AN: 152150Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000479 AC: 12AN: 250344Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135322
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GnomAD4 exome AF: 0.0000520 AC: 76AN: 1461126Hom.: 0 Cov.: 30 AF XY: 0.0000482 AC XY: 35AN XY: 726824
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GnomAD4 genome AF: 0.0000460 AC: 7AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74336
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Uncertain
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Uncertain
DANN
Uncertain
DEOGEN2
Benign
T;T;T;.;T;T;T
Eigen
Pathogenic
Eigen_PC
Pathogenic
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D;D;D;D;D
M_CAP
Uncertain
D
MetaRNN
Uncertain
D;D;D;D;D;D;D
MetaSVM
Uncertain
T
MutationAssessor
Uncertain
M;.;.;.;.;.;.
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Uncertain
D;D;D;.;D;D;D
REVEL
Uncertain
Sift
Uncertain
D;D;D;.;D;D;D
Sift4G
Uncertain
D;D;D;D;D;D;D
Polyphen
D;.;.;.;.;.;.
Vest4
MVP
MPC
ClinPred
D
GERP RS
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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