chr19-47197298-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005500.3(SAE1):c.799G>C(p.Glu267Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000372 in 1,613,908 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SAE1 | NM_005500.3 | c.799G>C | p.Glu267Gln | missense_variant | 7/9 | ENST00000270225.12 | |
SAE1 | NM_001145713.2 | c.734-11861G>C | intron_variant | ||||
SAE1 | NM_001145714.2 | c.734-6373G>C | intron_variant | ||||
SAE1 | NR_027280.2 | n.979G>C | non_coding_transcript_exon_variant | 7/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAE1 | ENST00000270225.12 | c.799G>C | p.Glu267Gln | missense_variant | 7/9 | 1 | NM_005500.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 31
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461738Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727190
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152170Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74328
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 08, 2024 | The c.799G>C (p.E267Q) alteration is located in exon 7 (coding exon 7) of the SAE1 gene. This alteration results from a G to C substitution at nucleotide position 799, causing the glutamic acid (E) at amino acid position 267 to be replaced by a glutamine (Q). 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