rs570378547
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000080.4(CHRNE):c.1383C>T(p.Ala461=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000626 in 1,597,372 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. A461A) has been classified as Likely benign.
Frequency
Consequence
NM_000080.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNE | NM_000080.4 | c.1383C>T | p.Ala461= | synonymous_variant | 12/12 | ENST00000649488.2 | |
CHRNE | XM_017024115.2 | c.1347C>T | p.Ala449= | synonymous_variant | 13/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNE | ENST00000649488.2 | c.1383C>T | p.Ala461= | synonymous_variant | 12/12 | NM_000080.4 | P1 | ||
CHRNE | ENST00000649830.1 | c.*19C>T | 3_prime_UTR_variant | 11/11 | |||||
CHRNE | ENST00000572438.1 | n.1069C>T | non_coding_transcript_exon_variant | 7/7 | 5 | ||||
CHRNE | ENST00000652550.1 | n.1109C>T | non_coding_transcript_exon_variant | 4/4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000924 AC: 2AN: 216426Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 116624
GnomAD4 exome AF: 0.00000415 AC: 6AN: 1445064Hom.: 0 Cov.: 34 AF XY: 0.00000418 AC XY: 3AN XY: 717162
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74482
ClinVar
Submissions by phenotype
Congenital myasthenic syndrome 4A Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 06, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at