10-21515556-C-A
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_207371.4(SKIDA1):c.2267G>T(p.Gly756Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000341 in 1,613,884 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_207371.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
SKIDA1 | NM_207371.4 | c.2267G>T | p.Gly756Val | missense_variant | Exon 4 of 4 | ENST00000449193.7 | NP_997254.3 | |
SKIDA1 | XM_047425204.1 | c.2267G>T | p.Gly756Val | missense_variant | Exon 2 of 2 | XP_047281160.1 | ||
SKIDA1 | XM_047425205.1 | c.2267G>T | p.Gly756Val | missense_variant | Exon 2 of 2 | XP_047281161.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
SKIDA1 | ENST00000449193.7 | c.2267G>T | p.Gly756Val | missense_variant | Exon 4 of 4 | 3 | NM_207371.4 | ENSP00000410041.2 | ||
SKIDA1 | ENST00000444772.3 | c.2030G>T | p.Gly677Val | missense_variant | Exon 2 of 2 | 5 | ENSP00000442432.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000241 AC: 6AN: 249258Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135220
GnomAD4 exome AF: 0.0000349 AC: 51AN: 1461706Hom.: 0 Cov.: 32 AF XY: 0.0000275 AC XY: 20AN XY: 727134
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.2267G>T (p.G756V) alteration is located in exon 4 (coding exon 1) of the SKIDA1 gene. This alteration results from a G to T substitution at nucleotide position 2267, causing the glycine (G) at amino acid position 756 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