1-152805279-C-A
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_178351.4(LCE1C):c.200G>T(p.Cys67Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000786 in 1,614,070 control chromosomes in the GnomAD database, including 12 homozygotes. In-silico tool predicts a benign outcome for this variant. 9/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0040 ( 2 hom., cov: 31)
Exomes 𝑓: 0.00045 ( 10 hom. )
Consequence
LCE1C
NM_178351.4 missense
NM_178351.4 missense
Scores
1
4
9
Clinical Significance
Conservation
PhyloP100: 2.90
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.008681148).
BP6
Variant 1-152805279-C-A is Benign according to our data. Variant chr1-152805279-C-A is described in ClinVar as [Benign]. Clinvar id is 775142.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High Homozygotes in GnomAd4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LCE1C | NM_178351.4 | c.200G>T | p.Cys67Phe | missense_variant | 2/2 | ENST00000607093.2 | |
LCE1C | NM_001276331.2 | c.110G>T | p.Cys37Phe | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
LCE1C | ENST00000607093.2 | c.200G>T | p.Cys67Phe | missense_variant | 2/2 | NM_178351.4 | P1 | ||
LCE1C | ENST00000606576.1 | c.110G>T | p.Cys37Phe | missense_variant | 3/3 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00400 AC: 609AN: 152188Hom.: 2 Cov.: 31
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GnomAD3 exomes AF: 0.00102 AC: 257AN: 250804Hom.: 3 AF XY: 0.000737 AC XY: 100AN XY: 135724
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GnomAD4 exome AF: 0.000452 AC: 660AN: 1461764Hom.: 10 Cov.: 33 AF XY: 0.000378 AC XY: 275AN XY: 727164
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GnomAD4 genome AF: 0.00400 AC: 609AN: 152306Hom.: 2 Cov.: 31 AF XY: 0.00384 AC XY: 286AN XY: 74476
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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 | Apr 04, 2018 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
DEOGEN2
Benign
T;.
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T;.
MetaRNN
Benign
T;T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M;.
MutationTaster
Benign
N
Sift4G
Pathogenic
D;.
Polyphen
D;.
Vest4
MVP
ClinPred
T
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