rs772271812
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS1
The NM_000079.4(CHRNA1):āc.536A>Gā(p.Asn179Ser) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000639 in 1,613,092 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_000079.4 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 |
---|---|---|---|---|---|---|---|
CHRNA1 | NM_000079.4 | c.536A>G | p.Asn179Ser | missense_variant | 5/9 | ENST00000348749.9 | |
CHRNA1 | NM_001039523.3 | c.611A>G | p.Asn204Ser | missense_variant | 6/10 | ||
CHRNA1 | XM_017003256.2 | c.632A>G | p.Asn211Ser | missense_variant | 5/9 | ||
CHRNA1 | XM_017003257.2 | c.557A>G | p.Asn186Ser | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA1 | ENST00000348749.9 | c.536A>G | p.Asn179Ser | missense_variant | 5/9 | 1 | NM_000079.4 | P1 | |
ENST00000442996.1 | n.322-18526T>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.000346 AC: 87AN: 251306Hom.: 0 AF XY: 0.000243 AC XY: 33AN XY: 135814
GnomAD4 exome AF: 0.0000664 AC: 97AN: 1460956Hom.: 0 Cov.: 32 AF XY: 0.0000523 AC XY: 38AN XY: 726804
GnomAD4 genome AF: 0.0000394 AC: 6AN: 152136Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74314
ClinVar
Submissions by phenotype
Lethal multiple pterygium syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jan 15, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at