NM_000745.4:c.713C>T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 4P and 2B. PM2PP3_ModerateBP6_Moderate
The NM_000745.4(CHRNA5):c.713C>T(p.Pro238Leu) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.000115 in 1,614,076 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000745.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHRNA5 | ENST00000299565.9 | c.713C>T | p.Pro238Leu | missense_variant | Exon 5 of 6 | 1 | NM_000745.4 | ENSP00000299565.5 | ||
CHRNA5 | ENST00000394802.4 | c.521+6C>T | splice_region_variant, intron_variant | Intron 4 of 4 | 3 | ENSP00000378281.4 | ||||
CHRNA5 | ENST00000559554.5 | c.458+255C>T | intron_variant | Intron 5 of 5 | 3 | ENSP00000453519.1 | ||||
ENSG00000261762 | ENST00000567141.1 | n.1173G>A | non_coding_transcript_exon_variant | Exon 1 of 1 | 6 |
Frequencies
GnomAD3 genomes AF: 0.0000986 AC: 15AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000916 AC: 23AN: 251168Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135750
GnomAD4 exome AF: 0.000117 AC: 171AN: 1461866Hom.: 0 Cov.: 31 AF XY: 0.000117 AC XY: 85AN XY: 727236
GnomAD4 genome AF: 0.0000985 AC: 15AN: 152210Hom.: 0 Cov.: 32 AF XY: 0.0000940 AC XY: 7AN XY: 74436
ClinVar
Submissions by phenotype
SMOKING AS A QUANTITATIVE TRAIT LOCUS 3 Uncertain:1
The CHRNA5 p.P238L variant was not identified in the literature nor was it identified in ClinVar. The variant was identified in dbSNP (ID: rs61742337) and in control databases in 25 of 282550 chromosomes at a frequency of 0.00008848, and was observed at the highest frequency in the European (non-Finnish) population in 24 of 128882 chromosomes (freq: 0.0001862) (Genome Aggregation Database March 6, 2019, v2.1.1).  The p.P238 residue is conserved in mammals and computational analyses (MUT Assesor, PolyPhen-2, SIFT, MutationTaster, Revel, FATHMM, MetaLR, DANN) suggest that the variant may impact the protein; however, this information is not predictive enough to assume pathogenicity. The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (Splice AI exome) do not predict a difference in splicing. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at