chr19-47150340-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_005500.3(SAE1):c.349A>G(p.Lys117Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000748 in 1,604,944 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005500.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAE1 | NM_005500.3 | c.349A>G | p.Lys117Glu | missense_variant | 3/9 | ENST00000270225.12 | |
SAE1 | NM_001145713.2 | c.349A>G | p.Lys117Glu | missense_variant | 3/7 | ||
SAE1 | NM_001145714.2 | c.349A>G | p.Lys117Glu | missense_variant | 3/8 | ||
SAE1 | NR_027280.2 | n.529A>G | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAE1 | ENST00000270225.12 | c.349A>G | p.Lys117Glu | missense_variant | 3/9 | 1 | NM_005500.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000456 AC: 11AN: 241032Hom.: 0 AF XY: 0.0000230 AC XY: 3AN XY: 130250
GnomAD4 exome AF: 0.00000757 AC: 11AN: 1452832Hom.: 0 Cov.: 30 AF XY: 0.00000415 AC XY: 3AN XY: 722428
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74296
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 08, 2022 | The c.349A>G (p.K117E) alteration is located in exon 3 (coding exon 3) of the SAE1 gene. This alteration results from a A to G substitution at nucleotide position 349, causing the lysine (K) at amino acid position 117 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at