X-108073260-C-T
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2
The NM_182607.5(VSIG1):c.579C>T(p.Thr193Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000289 in 1,209,061 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 9 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_182607.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
VSIG1 | ENST00000217957.10 | c.579C>T | p.Thr193Thr | synonymous_variant | Exon 5 of 7 | 1 | NM_182607.5 | ENSP00000217957.3 | ||
VSIG1 | ENST00000415430.7 | c.687C>T | p.Thr229Thr | synonymous_variant | Exon 6 of 8 | 2 | ENSP00000402219.3 | |||
VSIG1 | ENST00000479635.1 | n.48C>T | non_coding_transcript_exon_variant | Exon 2 of 2 | 3 | |||||
VSIG1 | ENST00000485533.1 | n.415C>T | non_coding_transcript_exon_variant | Exon 4 of 4 | 5 |
Frequencies
GnomAD3 genomes AF: 0.0000626 AC: 7AN: 111781Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33991
GnomAD3 exomes AF: 0.0000767 AC: 14AN: 182496Hom.: 0 AF XY: 0.000104 AC XY: 7AN XY: 66996
GnomAD4 exome AF: 0.0000255 AC: 28AN: 1097280Hom.: 0 Cov.: 29 AF XY: 0.0000248 AC XY: 9AN XY: 362678
GnomAD4 genome AF: 0.0000626 AC: 7AN: 111781Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33991
ClinVar
Submissions by phenotype
not provided Benign:1
VSIG1: BP4, BP7 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at