rs747061429

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_032048.3(EMILIN2):​c.598G>A​(p.Asp200Asn) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 32)

Consequence

EMILIN2
NM_032048.3 missense

Scores

2
5
12

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 7.76
Variant links:
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]
LPIN2 (HGNC:14450): (lipin 2) Mouse studies suggest that this gene functions during normal adipose tissue development and may play a role in human triglyceride metabolism. This gene represents a candidate gene for human lipodystrophy, characterized by loss of body fat, fatty liver, hypertriglyceridemia, and insulin resistance. [provided by RefSeq, Jul 2008]

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ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.27126992).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
EMILIN2NM_032048.3 linkc.598G>A p.Asp200Asn missense_variant Exon 4 of 8 ENST00000254528.4 NP_114437.2 Q9BXX0

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
EMILIN2ENST00000254528.4 linkc.598G>A p.Asp200Asn missense_variant Exon 4 of 8 1 NM_032048.3 ENSP00000254528.3 Q9BXX0
LPIN2ENST00000697039.1 linkc.2547-5291C>T intron_variant Intron 19 of 19 ENSP00000513061.1 A0A8V8TLW1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD4 exome
Cov.:
30
GnomAD4 genome
Cov.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.22
BayesDel_addAF
Benign
-0.17
T
BayesDel_noAF
Benign
-0.49
CADD
Benign
23
DANN
Pathogenic
1.0
DEOGEN2
Benign
0.062
T
Eigen
Uncertain
0.42
Eigen_PC
Uncertain
0.51
FATHMM_MKL
Pathogenic
0.99
D
LIST_S2
Benign
0.82
T
M_CAP
Benign
0.023
T
MetaRNN
Benign
0.27
T
MetaSVM
Benign
-0.93
T
MutationAssessor
Uncertain
2.8
M
PrimateAI
Benign
0.45
T
PROVEAN
Benign
-2.0
N
REVEL
Benign
0.12
Sift
Uncertain
0.017
D
Sift4G
Uncertain
0.0030
D
Polyphen
0.53
P
Vest4
0.34
MutPred
0.24
Gain of MoRF binding (P = 0.0334);
MVP
0.46
MPC
0.40
ClinPred
0.97
D
GERP RS
5.4
Varity_R
0.28
gMVP
0.36

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs747061429; hg19: chr18-2890723; API