1-109229480-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_006513.4(SARS1):c.355G>A(p.Ala119Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,614,218 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_006513.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SARS1 | NM_006513.4 | c.355G>A | p.Ala119Thr | missense_variant | 4/11 | ENST00000234677.7 | |
SARS1 | NM_001330669.1 | c.355G>A | p.Ala119Thr | missense_variant | 4/12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SARS1 | ENST00000234677.7 | c.355G>A | p.Ala119Thr | missense_variant | 4/11 | 1 | NM_006513.4 | P1 | |
SARS1 | ENST00000369923.4 | c.355G>A | p.Ala119Thr | missense_variant | 4/12 | 5 | |||
SARS1 | ENST00000477544.5 | n.380G>A | non_coding_transcript_exon_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000788 AC: 12AN: 152222Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000119 AC: 3AN: 251450Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135896
GnomAD4 exome AF: 0.0000144 AC: 21AN: 1461878Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 10AN XY: 727236
GnomAD4 genome ? AF: 0.0000788 AC: 12AN: 152340Hom.: 0 Cov.: 32 AF XY: 0.0000805 AC XY: 6AN XY: 74496
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 06, 2023 | The c.355G>A (p.A119T) alteration is located in exon 4 (coding exon 4) of the SARS gene. This alteration results from a G to A substitution at nucleotide position 355, causing the alanine (A) at amino acid position 119 to be replaced by a threonine (T). 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