17-4898835-G-C

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6BP7BS1BS2

The NM_000080.4(CHRNE):​c.1383C>G​(p.Ala461Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00115 in 1,597,374 control chromosomes in the GnomAD database, including 37 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).

Frequency

Genomes: š‘“ 0.00062 ( 0 hom., cov: 32)
Exomes š‘“: 0.0012 ( 37 hom. )

Consequence

CHRNE
NM_000080.4 synonymous

Scores

2

Clinical Significance

Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:1B:4

Conservation

PhyloP100: -6.13
Variant links:
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]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
Variant 17-4898835-G-C is Benign according to our data. Variant chr17-4898835-G-C is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 465860.We mark this variant Likely_benign, oryginal submissions are: {Likely_benign=1, Benign=2, Uncertain_significance=1}.
BP7
Synonymous conserved (PhyloP=-6.13 with no splicing effect.
BS1
Variant frequency is greater than expected in population sas. gnomad4 allele frequency = 0.000624 (95/152308) while in subpopulation SAS AF= 0.0189 (91/4822). AF 95% confidence interval is 0.0157. There are 0 homozygotes in gnomad4. There are 74 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High Homozygotes in GnomAdExome4 at 37 AD,AR gene

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
CHRNENM_000080.4 linkc.1383C>G p.Ala461Ala synonymous_variant Exon 12 of 12 ENST00000649488.2 NP_000071.1 Q04844
CHRNEXM_017024115.2 linkc.1347C>G p.Ala449Ala synonymous_variant Exon 13 of 13 XP_016879604.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
CHRNEENST00000649488.2 linkc.1383C>G p.Ala461Ala synonymous_variant Exon 12 of 12 NM_000080.4 ENSP00000497829.1 Q04844
CHRNEENST00000649830 linkc.*19C>G 3_prime_UTR_variant Exon 11 of 11 ENSP00000496907.1 A0A3B3IRM1
CHRNEENST00000572438.1 linkn.1069C>G non_coding_transcript_exon_variant Exon 7 of 7 5
CHRNEENST00000652550.1 linkn.1109C>G non_coding_transcript_exon_variant Exon 4 of 4

Frequencies

GnomAD3 genomes
AF:
0.000631
AC:
96
AN:
152190
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000724
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.0191
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.0000147
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.00274
AC:
592
AN:
216426
Hom.:
10
AF XY:
0.00360
AC XY:
420
AN XY:
116624
show subpopulations
Gnomad AFR exome
AF:
0.000149
Gnomad AMR exome
AF:
0.0000336
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0215
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.0000310
Gnomad OTH exome
AF:
0.000554
GnomAD4 exome
AF:
0.00121
AC:
1749
AN:
1445066
Hom.:
37
Cov.:
34
AF XY:
0.00172
AC XY:
1234
AN XY:
717164
show subpopulations
Gnomad4 AFR exome
AF:
0.0000600
Gnomad4 AMR exome
AF:
0.0000244
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0196
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00000905
Gnomad4 OTH exome
AF:
0.00154
GnomAD4 genome
AF:
0.000624
AC:
95
AN:
152308
Hom.:
0
Cov.:
32
AF XY:
0.000994
AC XY:
74
AN XY:
74482
show subpopulations
Gnomad4 AFR
AF:
0.0000722
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.0189
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.0000147
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.0000434
Hom.:
0
Bravo
AF:
0.000121
Asia WGS
AF:
0.00664
AC:
23
AN:
3478

ClinVar

Significance: Conflicting classifications of pathogenicity
Submissions summary: Uncertain:1Benign:4
Revision: criteria provided, conflicting classifications
LINK: link

Submissions by phenotype

Congenital myasthenic syndrome Uncertain:1Benign:1
Apr 27, 2017
Illumina Laboratory Services, Illumina
Significance: Uncertain significance
Review Status: criteria provided, single submitter
Collection Method: clinical testing

This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

Sep 16, 2020
Natera, Inc.
Significance: Benign
Review Status: no assertion criteria provided
Collection Method: clinical testing

- -

not specified Benign:1
Mar 30, 2021
Athena Diagnostics
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Congenital myasthenic syndrome 4A Benign:1
Dec 07, 2024
Labcorp Genetics (formerly Invitae), Labcorp
Significance: Benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

not provided Benign:1
Oct 27, 2021
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.83
CADD
Benign
0.090
DANN
Benign
0.85

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: rs570378547; hg19: chr17-4802130; API