chr4-100465486-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_016242.4(EMCN):c.313G>A(p.Val105Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0054 in 1,607,914 control chromosomes in the GnomAD database, including 149 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.018 ( 68 hom., cov: 32)
Exomes 𝑓: 0.0041 ( 81 hom. )
Consequence
EMCN
NM_016242.4 missense
NM_016242.4 missense
Scores
18
Clinical Significance
Conservation
PhyloP100: -2.67
Genes affected
EMCN (HGNC:16041): (endomucin) EMCN is a mucin-like sialoglycoprotein that interferes with the assembly of focal adhesion complexes and inhibits interaction between cells and the extracellular matrix (Kinoshita et al., 2001 [PubMed 11418125]).[supplied by OMIM, Mar 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (MetaRNN=0.0028885603).
BP6
?
Variant 4-100465486-C-T is Benign according to our data. Variant chr4-100465486-C-T is described in ClinVar as [Benign]. Clinvar id is 776002.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0545 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMCN | NM_016242.4 | c.313G>A | p.Val105Ile | missense_variant | 4/12 | ENST00000296420.9 | |
LOC124900740 | XR_007058203.1 | n.68+44048C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMCN | ENST00000296420.9 | c.313G>A | p.Val105Ile | missense_variant | 4/12 | 1 | NM_016242.4 | P1 | |
ENST00000652064.1 | n.309-7948C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0177 AC: 2688AN: 152056Hom.: 68 Cov.: 32
GnomAD3 genomes
?
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GnomAD3 exomes AF: 0.00620 AC: 1546AN: 249516Hom.: 39 AF XY: 0.00518 AC XY: 699AN XY: 135022
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GnomAD4 exome AF: 0.00411 AC: 5979AN: 1455742Hom.: 81 Cov.: 29 AF XY: 0.00390 AC XY: 2827AN XY: 724138
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GnomAD4 genome ? AF: 0.0178 AC: 2705AN: 152172Hom.: 68 Cov.: 32 AF XY: 0.0171 AC XY: 1269AN XY: 74386
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ESP6500AA
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256
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ExAC
?
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907
Asia WGS
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AN:
3478
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 03, 2018 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
DEOGEN2
Benign
T;.;.;.;.
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T
MetaRNN
Benign
T;T;T;T;T
MetaSVM
Benign
T
MutationAssessor
Benign
N;N;.;N;.
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N;N;N;N
REVEL
Benign
Sift
Benign
T;T;T;T;T
Sift4G
Benign
T;T;T;T;T
Polyphen
B;B;.;.;.
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