chr4-87494210-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_004684.6(SPARCL1):c.590T>C(p.Ile197Thr) 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 1,613,924 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_004684.6 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 |
---|---|---|---|---|---|---|---|
SPARCL1 | NM_004684.6 | c.590T>C | p.Ile197Thr | missense_variant | 4/11 | ENST00000282470.11 | |
SPARCL1 | NM_001128310.3 | c.590T>C | p.Ile197Thr | missense_variant | 5/12 | ||
SPARCL1 | NM_001291976.2 | c.215T>C | p.Ile72Thr | missense_variant | 5/12 | ||
SPARCL1 | NM_001291977.2 | c.215T>C | p.Ile72Thr | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPARCL1 | ENST00000282470.11 | c.590T>C | p.Ile197Thr | missense_variant | 4/11 | 1 | NM_004684.6 | P2 | |
SPARCL1 | ENST00000418378.5 | c.590T>C | p.Ile197Thr | missense_variant | 5/12 | 5 | P2 | ||
SPARCL1 | ENST00000503414.5 | c.215T>C | p.Ile72Thr | missense_variant | 5/12 | 2 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250998Hom.: 0 AF XY: 0.00000737 AC XY: 1AN XY: 135642
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1461856Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 727218
GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152068Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74264
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 23, 2024 | The c.590T>C (p.I197T) alteration is located in exon 5 (coding exon 3) of the SPARCL1 gene. This alteration results from a T to C substitution at nucleotide position 590, causing the isoleucine (I) at amino acid position 197 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