3-113584751-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_017699.3(SIDT1):āc.889A>Gā(p.Ile297Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000208 in 1,443,156 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 (ā ).
Frequency
Consequence
NM_017699.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SIDT1 | ENST00000264852.9 | c.889A>G | p.Ile297Val | missense_variant | 8/25 | 2 | NM_017699.3 | ENSP00000264852.4 | ||
SIDT1 | ENST00000393830.4 | c.889A>G | p.Ile297Val | missense_variant | 8/26 | 1 | ENSP00000377416.4 | |||
SIDT1 | ENST00000488390.1 | n.70A>G | non_coding_transcript_exon_variant | 1/4 | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 exomes AF: 0.00000430 AC: 1AN: 232554Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 125686
GnomAD4 exome AF: 0.00000208 AC: 3AN: 1443156Hom.: 0 Cov.: 29 AF XY: 0.00000279 AC XY: 2AN XY: 717416
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 13, 2024 | The c.889A>G (p.I297V) alteration is located in exon 8 (coding exon 8) of the SIDT1 gene. This alteration results from a A to G substitution at nucleotide position 889, causing the isoleucine (I) at amino acid position 297 to be replaced by a valine (V). 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