chr18-2885112-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_032048.3(EMILIN2):c.406C>T(p.Pro136Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00201 in 1,609,258 control chromosomes in the GnomAD database, including 70 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.011 ( 37 hom., cov: 33)
Exomes 𝑓: 0.0011 ( 33 hom. )
Consequence
EMILIN2
NM_032048.3 missense
NM_032048.3 missense
Scores
1
7
10
Clinical Significance
Conservation
PhyloP100: 3.10
Genes affected
EMILIN2 (HGNC:19881): (elastin microfibril interfacer 2) Predicted to enable extracellular matrix constituent conferring elasticity. Predicted to be involved in cell adhesion. Located in extracellular region. [provided by Alliance of Genome Resources, Apr 2022]
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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=0.0052028).
BP6
?
Variant 18-2885112-C-T is Benign according to our data. Variant chr18-2885112-C-T is described in ClinVar as [Benign]. Clinvar id is 781394.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0108 (1646/152294) while in subpopulation AFR AF= 0.0363 (1507/41566). AF 95% confidence interval is 0.0347. There are 37 homozygotes in gnomad4. There are 759 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 37 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
EMILIN2 | NM_032048.3 | c.406C>T | p.Pro136Ser | missense_variant | 3/8 | ENST00000254528.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
EMILIN2 | ENST00000254528.4 | c.406C>T | p.Pro136Ser | missense_variant | 3/8 | 1 | NM_032048.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0108 AC: 1648AN: 152176Hom.: 37 Cov.: 33
GnomAD3 genomes
?
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1648
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33
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GnomAD3 exomes AF: 0.00297 AC: 732AN: 246222Hom.: 17 AF XY: 0.00220 AC XY: 293AN XY: 133300
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GnomAD4 exome AF: 0.00109 AC: 1593AN: 1456964Hom.: 33 Cov.: 30 AF XY: 0.000934 AC XY: 677AN XY: 724762
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GnomAD4 genome ? AF: 0.0108 AC: 1646AN: 152294Hom.: 37 Cov.: 33 AF XY: 0.0102 AC XY: 759AN XY: 74474
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?
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433
Asia WGS
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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 | Dec 31, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Uncertain
Dann
Pathogenic
DEOGEN2
Benign
T
Eigen
Uncertain
Eigen_PC
Uncertain
FATHMM_MKL
Uncertain
D
LIST_S2
Benign
T
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Benign
T
PROVEAN
Uncertain
D
REVEL
Benign
Sift
Uncertain
D
Sift4G
Uncertain
D
Polyphen
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