8-61299931-T-C
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_173519.3(CLVS1):c.104T>C(p.Ile35Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000186 in 1,613,894 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173519.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLVS1 | NM_173519.3 | c.104T>C | p.Ile35Thr | missense_variant | 2/6 | ENST00000325897.5 | |
CLVS1 | XM_017013141.2 | c.104T>C | p.Ile35Thr | missense_variant | 3/7 | ||
CLVS1 | XM_017013142.3 | c.104T>C | p.Ile35Thr | missense_variant | 3/7 | ||
CLVS1 | XM_024447079.2 | c.104T>C | p.Ile35Thr | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLVS1 | ENST00000325897.5 | c.104T>C | p.Ile35Thr | missense_variant | 2/6 | 1 | NM_173519.3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461734Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 727164
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152160Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 26, 2023 | The c.104T>C (p.I35T) alteration is located in exon 2 (coding exon 1) of the CLVS1 gene. This alteration results from a T to C substitution at nucleotide position 104, causing the isoleucine (I) at amino acid position 35 to be replaced by a threonine (T). 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