chr20-63350253-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_000744.7(CHRNA4):c.1158C>T(p.Pro386=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000186 in 1,609,740 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. P386P) has been classified as Likely benign.
Frequency
Consequence
NM_000744.7 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA4 | NM_000744.7 | c.1158C>T | p.Pro386= | synonymous_variant | 5/6 | ENST00000370263.9 | |
CHRNA4 | NM_001256573.2 | c.630C>T | p.Pro210= | synonymous_variant | 5/6 | ||
CHRNA4 | NR_046317.2 | n.1367C>T | non_coding_transcript_exon_variant | 5/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA4 | ENST00000370263.9 | c.1158C>T | p.Pro386= | synonymous_variant | 5/6 | 1 | NM_000744.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152184Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000420 AC: 10AN: 238310Hom.: 0 AF XY: 0.0000460 AC XY: 6AN XY: 130510
GnomAD4 exome AF: 0.0000124 AC: 18AN: 1457438Hom.: 0 Cov.: 99 AF XY: 0.0000152 AC XY: 11AN XY: 724814
GnomAD4 genome AF: 0.0000788 AC: 12AN: 152302Hom.: 0 Cov.: 32 AF XY: 0.0000806 AC XY: 6AN XY: 74470
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | CHRNA4: BP4, BP7 - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 26, 2020 | - - |
Autosomal dominant nocturnal frontal lobe epilepsy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 04, 2023 | - - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 30, 2018 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at