10-70435589-G-A
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP7BS2
The NM_018055.5(NODAL):c.588C>T(p.Leu196=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,952 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Synonymous variant affecting the same amino acid position (i.e. L196L) has been classified as Benign.
Frequency
Consequence
NM_018055.5 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 |
---|---|---|---|---|---|---|---|
NODAL | NM_018055.5 | c.588C>T | p.Leu196= | synonymous_variant | 2/3 | ENST00000287139.8 | |
NODAL | NM_001329906.2 | c.189C>T | p.Leu63= | synonymous_variant | 2/3 | ||
NODAL | XM_024448028.2 | c.189C>T | p.Leu63= | synonymous_variant | 2/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NODAL | ENST00000287139.8 | c.588C>T | p.Leu196= | synonymous_variant | 2/3 | 1 | NM_018055.5 | P1 | |
NODAL | ENST00000414871.1 | c.423C>T | p.Leu141= | synonymous_variant | 2/3 | 1 | |||
ENST00000624563.1 | n.761G>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461784Hom.: 0 Cov.: 29 AF XY: 0.00000413 AC XY: 3AN XY: 727202
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74346
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at