chr4-87493950-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_004684.6(SPARCL1):c.850G>A(p.Val284Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000266 in 1,614,140 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 Likely benign (★).
Frequency
Consequence
NM_004684.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPARCL1 | NM_004684.6 | c.850G>A | p.Val284Ile | missense_variant | 4/11 | ENST00000282470.11 | |
SPARCL1 | NM_001128310.3 | c.850G>A | p.Val284Ile | missense_variant | 5/12 | ||
SPARCL1 | NM_001291976.2 | c.475G>A | p.Val159Ile | missense_variant | 5/12 | ||
SPARCL1 | NM_001291977.2 | c.475G>A | p.Val159Ile | missense_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPARCL1 | ENST00000282470.11 | c.850G>A | p.Val284Ile | missense_variant | 4/11 | 1 | NM_004684.6 | P2 | |
SPARCL1 | ENST00000418378.5 | c.850G>A | p.Val284Ile | missense_variant | 5/12 | 5 | P2 | ||
SPARCL1 | ENST00000503414.5 | c.475G>A | p.Val159Ile | missense_variant | 5/12 | 2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152164Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000438 AC: 11AN: 251284Hom.: 0 AF XY: 0.0000368 AC XY: 5AN XY: 135814
GnomAD4 exome AF: 0.0000274 AC: 40AN: 1461858Hom.: 0 Cov.: 32 AF XY: 0.0000303 AC XY: 22AN XY: 727224
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152282Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74466
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 30, 2022 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at