rs759534966
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_StrongBP6_ModerateBP7
The NM_000079.4(CHRNA1):c.648C>T(p.Thr216=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,613,988 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. T216T) has been classified as Likely benign.
Frequency
Consequence
NM_000079.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CHRNA1 | NM_000079.4 | c.648C>T | p.Thr216= | synonymous_variant | 6/9 | ENST00000348749.9 | |
CHRNA1 | NM_001039523.3 | c.723C>T | p.Thr241= | synonymous_variant | 7/10 | ||
CHRNA1 | XM_017003256.2 | c.744C>T | p.Thr248= | synonymous_variant | 6/9 | ||
CHRNA1 | XM_017003257.2 | c.669C>T | p.Thr223= | synonymous_variant | 5/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CHRNA1 | ENST00000348749.9 | c.648C>T | p.Thr216= | synonymous_variant | 6/9 | 1 | NM_000079.4 | P1 | |
ENST00000442996.1 | n.322-19116G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152096Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000517 AC: 13AN: 251456Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135908
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1461892Hom.: 0 Cov.: 31 AF XY: 0.0000124 AC XY: 9AN XY: 727246
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152096Hom.: 0 Cov.: 31 AF XY: 0.0000269 AC XY: 2AN XY: 74286
ClinVar
Submissions by phenotype
Lethal multiple pterygium syndrome Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Jul 20, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at