rs1049544
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_004684.6(SPARCL1):āc.316C>Gā(p.His106Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.404 in 1,613,206 control chromosomes in the GnomAD database, including 141,115 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.316C>G | p.His106Asp | missense_variant | 4/11 | ENST00000282470.11 | |
SPARCL1 | NM_001128310.3 | c.316C>G | p.His106Asp | missense_variant | 5/12 | ||
SPARCL1 | NM_001291976.2 | c.-60C>G | 5_prime_UTR_variant | 5/12 | |||
SPARCL1 | NM_001291977.2 | c.-60C>G | 5_prime_UTR_variant | 3/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SPARCL1 | ENST00000282470.11 | c.316C>G | p.His106Asp | missense_variant | 4/11 | 1 | NM_004684.6 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.513 AC: 77841AN: 151774Hom.: 22723 Cov.: 32
GnomAD3 exomes AF: 0.450 AC: 112968AN: 251110Hom.: 27347 AF XY: 0.445 AC XY: 60415AN XY: 135704
GnomAD4 exome AF: 0.392 AC: 573160AN: 1461314Hom.: 118349 Cov.: 39 AF XY: 0.396 AC XY: 288175AN XY: 726958
GnomAD4 genome ? AF: 0.513 AC: 77938AN: 151892Hom.: 22766 Cov.: 32 AF XY: 0.515 AC XY: 38219AN XY: 74212
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at