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):āc.1383C>Gā(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
Consequence
NM_000080.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNE | ENST00000649488.2 | c.1383C>G | p.Ala461Ala | synonymous_variant | Exon 12 of 12 | NM_000080.4 | ENSP00000497829.1 | |||
CHRNE | ENST00000649830 | c.*19C>G | 3_prime_UTR_variant | Exon 11 of 11 | ENSP00000496907.1 | |||||
CHRNE | ENST00000572438.1 | n.1069C>G | non_coding_transcript_exon_variant | Exon 7 of 7 | 5 | |||||
CHRNE | ENST00000652550.1 | n.1109C>G | non_coding_transcript_exon_variant | Exon 4 of 4 |
Frequencies
GnomAD3 genomes AF: 0.000631 AC: 96AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00274 AC: 592AN: 216426Hom.: 10 AF XY: 0.00360 AC XY: 420AN XY: 116624
GnomAD4 exome AF: 0.00121 AC: 1749AN: 1445066Hom.: 37 Cov.: 34 AF XY: 0.00172 AC XY: 1234AN XY: 717164
GnomAD4 genome AF: 0.000624 AC: 95AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000994 AC XY: 74AN XY: 74482
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome Uncertain:1Benign:1
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. -
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not specified Benign:1
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Congenital myasthenic syndrome 4A Benign:1
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not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at