rs547033777
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_005585.5(SMAD6):c.264C>A(p.Gly88=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000246 in 1,219,698 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. G88G) has been classified as Likely benign.
Frequency
Consequence
NM_005585.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SMAD6 | NM_005585.5 | c.264C>A | p.Gly88= | synonymous_variant | 1/4 | ENST00000288840.10 | |
SMAD6 | NR_027654.2 | n.1287C>A | non_coding_transcript_exon_variant | 1/5 | |||
SMAD6 | XR_931827.3 | n.1287C>A | non_coding_transcript_exon_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SMAD6 | ENST00000288840.10 | c.264C>A | p.Gly88= | synonymous_variant | 1/4 | 1 | NM_005585.5 | P1 | |
SMAD6 | ENST00000557916.5 | c.264C>A | p.Gly88= | synonymous_variant, NMD_transcript_variant | 1/5 | 1 | |||
SMAD6 | ENST00000612349.1 | n.446C>A | non_coding_transcript_exon_variant | 1/1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000132 AC: 2AN: 151162Hom.: 0 Cov.: 33
GnomAD4 exome AF: 9.36e-7 AC: 1AN: 1068536Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 505562
GnomAD4 genome ? AF: 0.0000132 AC: 2AN: 151162Hom.: 0 Cov.: 33 AF XY: 0.0000271 AC XY: 2AN XY: 73818
ClinVar
Submissions by phenotype
Aortic valve disease 2 Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 01, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at