rs13051
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004684.6(SPARCL1):c.146C>A(p.Ala49Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.403 in 1,608,716 control chromosomes in the GnomAD database, including 140,871 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_004684.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SPARCL1 | NM_004684.6 | c.146C>A | p.Ala49Asp | missense_variant | 3/11 | ENST00000282470.11 | |
SPARCL1 | NM_001128310.3 | c.146C>A | p.Ala49Asp | missense_variant | 4/12 | ||
SPARCL1 | NM_001291976.2 | c.-230C>A | 5_prime_UTR_variant | 4/12 | |||
SPARCL1 | NM_001291977.2 | c.-141-471C>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPARCL1 | ENST00000282470.11 | c.146C>A | p.Ala49Asp | missense_variant | 3/11 | 1 | NM_004684.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.513 AC: 77955AN: 152022Hom.: 22774 Cov.: 33
GnomAD3 exomes AF: 0.449 AC: 112080AN: 249676Hom.: 27137 AF XY: 0.444 AC XY: 59942AN XY: 134954
GnomAD4 exome AF: 0.392 AC: 570514AN: 1456576Hom.: 118054 Cov.: 33 AF XY: 0.396 AC XY: 286965AN XY: 724788
GnomAD4 genome AF: 0.513 AC: 78052AN: 152140Hom.: 22817 Cov.: 33 AF XY: 0.515 AC XY: 38305AN XY: 74374
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at