X-108067084-C-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_182607.5(VSIG1):āc.362C>Gā(p.Pro121Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000138 in 1,209,436 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 48 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_182607.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VSIG1 | ENST00000217957.10 | c.362C>G | p.Pro121Arg | missense_variant | Exon 3 of 7 | 1 | NM_182607.5 | ENSP00000217957.3 | ||
VSIG1 | ENST00000415430.7 | c.470C>G | p.Pro157Arg | missense_variant | Exon 4 of 8 | 2 | ENSP00000402219.3 | |||
VSIG1 | ENST00000458383.1 | c.470C>G | p.Pro157Arg | missense_variant | Exon 4 of 4 | 4 | ENSP00000407102.1 | |||
VSIG1 | ENST00000485533.1 | n.198C>G | non_coding_transcript_exon_variant | Exon 2 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000988 AC: 11AN: 111370Hom.: 0 Cov.: 22 AF XY: 0.0000893 AC XY: 3AN XY: 33592
GnomAD3 exomes AF: 0.0000982 AC: 18AN: 183388Hom.: 0 AF XY: 0.000103 AC XY: 7AN XY: 67852
GnomAD4 exome AF: 0.000142 AC: 156AN: 1098066Hom.: 0 Cov.: 31 AF XY: 0.000124 AC XY: 45AN XY: 363526
GnomAD4 genome AF: 0.0000988 AC: 11AN: 111370Hom.: 0 Cov.: 22 AF XY: 0.0000893 AC XY: 3AN XY: 33592
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.470C>G (p.P157R) alteration is located in exon 4 (coding exon 4) of the VSIG1 gene. This alteration results from a C to G substitution at nucleotide position 470, causing the proline (P) at amino acid position 157 to be replaced by an arginine (R). 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