chr17-4899300-A-C

Position:

• chr17-4899300-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_000080.4(CHRNE):​c.1117T>G​(p.Ser373Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. S373S) has been classified as Benign.

• Frequency: Genomes: not found (cov: 32)
• Consequence: CHRNE NM_000080.4 missense
• Clinical Significance: Uncertain significance criteria provided, single submitter U:1
• Conservation: PhyloP100: 0.608

Genes affected

CHRNE (HGNC:1966): (cholinergic receptor nicotinic epsilon subunit) Acetylcholine receptors at mature mammalian neuromuscular junctions are pentameric protein complexes composed of four subunits in the ratio of two alpha subunits to one beta, one epsilon, and one delta subunit. The acetylcholine receptor changes subunit composition shortly after birth when the epsilon subunit replaces the gamma subunit seen in embryonic receptors. Mutations in the epsilon subunit are associated with congenital myasthenic syndrome. [provided by RefSeq, Sep 2009]

ACMG classification

Verdict is Uncertain_significance. Variant got 2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CHRNE	NM_000080.4	c.1117T>G	p.Ser373Ala	missense_variant	10/12	ENST00000649488.2
CHRNE	XM_017024115.2	c.1081T>G	p.Ser361Ala	missense_variant	11/13

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CHRNE	ENST00000649488.2	c.1117T>G	p.Ser373Ala	missense_variant	10/12		NM_000080.4	P1
CHRNE	ENST00000649830.1	c.184T>G	p.Ser62Ala	missense_variant	10/11
CHRNE	ENST00000572438.1	n.803T>G		non_coding_transcript_exon_variant	5/7	5
CHRNE	ENST00000652550.1	n.847T>G		non_coding_transcript_exon_variant	2/4

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 35

GnomAD4 genome Cov.: 32

ClinVar

Significance: Uncertain significance

Submissions summary: Uncertain:1

Revision: criteria provided, single submitter

Submissions by phenotype

Congenital myasthenic syndrome 4A Uncertain:1

Uncertain significance, criteria provided, single submitter

clinical testing

Invitae

Jun 13, 2022

In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CHRNE protein function. ClinVar contains an entry for this variant (Variation ID: 534257). This variant has not been reported in the literature in individuals affected with CHRNE-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change replaces serine, which is neutral and polar, with alanine, which is neutral and non-polar, at codon 373 of the CHRNE protein (p.Ser373Ala). -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.14
BayesDel_addAF	Benign	-0.072	T
BayesDel_noAF	Benign	-0.34
CADD	Benign	22
DANN	Uncertain	0.99
DEOGEN2	Uncertain	0.42	T;T;.
Eigen	Uncertain	0.37
Eigen_PC	Uncertain	0.27
FATHMM_MKL	Benign	0.70	D
LIST_S2	Benign	0.57	.;T;T
M_CAP	Pathogenic	0.83	D
MetaRNN	Uncertain	0.43	T;T;T
MetaSVM	Uncertain	-0.0096	T
MutationAssessor	Uncertain	2.3	M;M;.
MutationTaster	Benign	0.97	N
PrimateAI	Pathogenic	0.84	D
PROVEAN	Benign	-2.2	N;.;.
REVEL	Uncertain	0.32
Sift	Uncertain	0.015	D;.;.
Sift4G	Uncertain	0.048	D;.;.
Polyphen		0.98	D;D;.
Vest4		0.36
MutPred		0.30		Loss of phosphorylation at S373 (P = 0.0013);Loss of phosphorylation at S373 (P = 0.0013);.;
MVP		0.92
MPC		0.57
ClinPred		0.97	D
GERP RS		4.7
Varity_R		0.28
gMVP		0.43

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

Other links and lift over

dbSNP: rs1555546304; hg19: chr17-4802595;