chr2-174748683-A-G
Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6BS1BS2
The NM_000079.4(CHRNA1):āc.1139T>Cā(p.Met380Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000188 in 1,614,220 control chromosomes in the GnomAD database, including 2 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 Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_000079.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -13 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA1 | NM_000079.4 | c.1139T>C | p.Met380Thr | missense_variant | 8/9 | ENST00000348749.9 | |
CHRNA1 | NM_001039523.3 | c.1214T>C | p.Met405Thr | missense_variant | 9/10 | ||
CHRNA1 | XM_017003256.2 | c.1235T>C | p.Met412Thr | missense_variant | 8/9 | ||
CHRNA1 | XM_017003257.2 | c.1160T>C | p.Met387Thr | missense_variant | 7/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA1 | ENST00000348749.9 | c.1139T>C | p.Met380Thr | missense_variant | 8/9 | 1 | NM_000079.4 | P1 | |
ENST00000442996.1 | n.321+18859A>G | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.000769 AC: 117AN: 152210Hom.: 2 Cov.: 33
GnomAD3 exomes AF: 0.000251 AC: 63AN: 251464Hom.: 0 AF XY: 0.000213 AC XY: 29AN XY: 135904
GnomAD4 exome AF: 0.000127 AC: 185AN: 1461892Hom.: 0 Cov.: 33 AF XY: 0.0000935 AC XY: 68AN XY: 727246
GnomAD4 genome AF: 0.000775 AC: 118AN: 152328Hom.: 2 Cov.: 33 AF XY: 0.000792 AC XY: 59AN XY: 74488
ClinVar
Submissions by phenotype
not provided Uncertain:2
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Jan 07, 2018 | - - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Jun 27, 2019 | - - |
Lethal multiple pterygium syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 13, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at