chr3-113608165-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_017699.3(SIDT1):c.1550G>A(p.Arg517His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000267 in 1,611,688 control chromosomes in the GnomAD database, with no homozygous occurrence. 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_017699.3 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 |
---|---|---|---|---|---|---|---|
SIDT1 | NM_017699.3 | c.1550G>A | p.Arg517His | missense_variant | 16/25 | ENST00000264852.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SIDT1 | ENST00000264852.9 | c.1550G>A | p.Arg517His | missense_variant | 16/25 | 2 | NM_017699.3 | P4 | |
SIDT1 | ENST00000393830.4 | c.1550G>A | p.Arg517His | missense_variant | 16/26 | 1 | A2 | ||
SIDT1 | ENST00000463226.1 | n.386G>A | non_coding_transcript_exon_variant | 5/15 | 2 | ||||
SIDT1 | ENST00000492863.1 | downstream_gene_variant | 3 |
Frequencies
GnomAD3 genomes AF: 0.0000921 AC: 14AN: 152046Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000322 AC: 8AN: 248672Hom.: 0 AF XY: 0.0000297 AC XY: 4AN XY: 134468
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1459524Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 726012
GnomAD4 genome AF: 0.000112 AC: 17AN: 152164Hom.: 0 Cov.: 32 AF XY: 0.000148 AC XY: 11AN XY: 74382
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 16, 2024 | The c.1550G>A (p.R517H) alteration is located in exon 16 (coding exon 16) of the SIDT1 gene. This alteration results from a G to A substitution at nucleotide position 1550, causing the arginine (R) at amino acid position 517 to be replaced by a histidine (H). 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