rs1059559
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_199161.5(SAA1):āc.256T>Cā(p.Phe86Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000239 in 1,614,008 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_199161.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAA1 | NM_199161.5 | c.256T>C | p.Phe86Leu | missense_variant | 4/4 | ENST00000356524.9 | |
SAA1 | NM_000331.6 | c.256T>C | p.Phe86Leu | missense_variant | 4/4 | ||
SAA1 | NM_001178006.3 | c.256T>C | p.Phe86Leu | missense_variant | 5/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAA1 | ENST00000356524.9 | c.256T>C | p.Phe86Leu | missense_variant | 4/4 | 1 | NM_199161.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00104 AC: 159AN: 152204Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000386 AC: 97AN: 251264Hom.: 0 AF XY: 0.000258 AC XY: 35AN XY: 135816
GnomAD4 exome AF: 0.000155 AC: 226AN: 1461686Hom.: 0 Cov.: 31 AF XY: 0.000157 AC XY: 114AN XY: 727160
GnomAD4 genome ? AF: 0.00105 AC: 160AN: 152322Hom.: 0 Cov.: 33 AF XY: 0.00109 AC XY: 81AN XY: 74492
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Apr 16, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at