chr15-78601522-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_000743.5(CHRNA3):c.1120G>A(p.Gly374Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000199 in 1,614,126 control chromosomes in the GnomAD database, including 5 homozygotes. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000743.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA3 | NM_000743.5 | c.1120G>A | p.Gly374Ser | missense_variant | 5/6 | ENST00000326828.6 | |
CHRNA3 | NM_001166694.2 | c.1120G>A | p.Gly374Ser | missense_variant | 5/6 | ||
CHRNA3 | XM_006720382.4 | c.919G>A | p.Gly307Ser | missense_variant | 5/6 | ||
CHRNA3 | NR_046313.2 | n.1322G>A | non_coding_transcript_exon_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA3 | ENST00000326828.6 | c.1120G>A | p.Gly374Ser | missense_variant | 5/6 | 1 | NM_000743.5 | P1 | |
CHRNA3 | ENST00000348639.7 | c.1120G>A | p.Gly374Ser | missense_variant | 5/6 | 1 | |||
CHRNA3 | ENST00000559658.5 | c.1120G>A | p.Gly374Ser | missense_variant, NMD_transcript_variant | 5/8 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.000454 AC: 69AN: 152116Hom.: 1 Cov.: 31
GnomAD3 exomes AF: 0.000633 AC: 159AN: 251248Hom.: 0 AF XY: 0.000538 AC XY: 73AN XY: 135798
GnomAD4 exome AF: 0.000172 AC: 251AN: 1461892Hom.: 4 Cov.: 31 AF XY: 0.000165 AC XY: 120AN XY: 727246
GnomAD4 genome ? AF: 0.000460 AC: 70AN: 152234Hom.: 1 Cov.: 31 AF XY: 0.000417 AC XY: 31AN XY: 74428
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 16, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at