chr1-117013649-T-C
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate
The NM_001256106.3(CD101):c.1085T>C(p.Leu362Pro) variant causes a missense change. The variant allele was found at a frequency of 0.000439 in 1,614,014 control chromosomes in the GnomAD database, including 4 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.00057 ( 1 hom., cov: 32)
Exomes 𝑓: 0.00043 ( 3 hom. )
Consequence
CD101
NM_001256106.3 missense
NM_001256106.3 missense
Scores
5
7
7
Clinical Significance
Conservation
PhyloP100: 6.03
Genes affected
CD101 (HGNC:5949): (CD101 molecule) Predicted to enable hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides. Predicted to be involved in cell surface receptor signaling pathway. Predicted to act upstream of or within positive regulation of myeloid leukocyte differentiation. Located in extracellular exosome. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.04651645).
BP6
?
Variant 1-117013649-T-C is Benign according to our data. Variant chr1-117013649-T-C is described in ClinVar as [Benign]. Clinvar id is 728107.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD101 | NM_001256106.3 | c.1085T>C | p.Leu362Pro | missense_variant | 4/10 | ENST00000682167.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD101 | ENST00000682167.1 | c.1085T>C | p.Leu362Pro | missense_variant | 4/10 | NM_001256106.3 | P1 | ||
CD101 | ENST00000369470.1 | c.1085T>C | p.Leu362Pro | missense_variant | 4/10 | 1 | P1 | ||
CD101 | ENST00000256652.8 | c.1085T>C | p.Leu362Pro | missense_variant | 4/9 | 2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000572 AC: 87AN: 152144Hom.: 1 Cov.: 32
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?
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GnomAD3 exomes AF: 0.000837 AC: 210AN: 250798Hom.: 1 AF XY: 0.000841 AC XY: 114AN XY: 135510
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GnomAD4 exome AF: 0.000425 AC: 622AN: 1461870Hom.: 3 Cov.: 31 AF XY: 0.000443 AC XY: 322AN XY: 727228
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GnomAD4 genome ? AF: 0.000572 AC: 87AN: 152144Hom.: 1 Cov.: 32 AF XY: 0.000552 AC XY: 41AN XY: 74316
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | May 16, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Benign
T
BayesDel_noAF
Uncertain
Cadd
Pathogenic
Dann
Pathogenic
DEOGEN2
Uncertain
D;D
Eigen
Pathogenic
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.
M_CAP
Benign
D
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Pathogenic
M;M
MutationTaster
Benign
D;D
PrimateAI
Benign
T
PROVEAN
Pathogenic
D;D
REVEL
Uncertain
Sift
Uncertain
D;D
Sift4G
Uncertain
D;D
Polyphen
D;D
Vest4
MVP
MPC
ClinPred
T
GERP RS
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