chr19-47150242-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_005500.3(SAE1):c.251C>A(p.Thr84Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000124 in 1,612,552 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 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.251C>A | p.Thr84Asn | missense_variant | 3/9 | ENST00000270225.12 | |
SAE1 | NM_001145713.2 | c.251C>A | p.Thr84Asn | missense_variant | 3/7 | ||
SAE1 | NM_001145714.2 | c.251C>A | p.Thr84Asn | missense_variant | 3/8 | ||
SAE1 | NR_027280.2 | n.431C>A | non_coding_transcript_exon_variant | 3/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SAE1 | ENST00000270225.12 | c.251C>A | p.Thr84Asn | missense_variant | 3/9 | 1 | NM_005500.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000559 AC: 14AN: 250574Hom.: 1 AF XY: 0.0000664 AC XY: 9AN XY: 135484
GnomAD4 exome AF: 0.0000116 AC: 17AN: 1460416Hom.: 1 Cov.: 30 AF XY: 0.0000110 AC XY: 8AN XY: 726534
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152136Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 17, 2021 | The c.251C>A (p.T84N) alteration is located in exon 3 (coding exon 3) of the SAE1 gene. This alteration results from a C to A substitution at nucleotide position 251, causing the threonine (T) at amino acid position 84 to be replaced by an asparagine (N). 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