chr10-100356554-A-C
Variant summary
Our verdict is Benign. Variant got -11 ACMG points: 1P and 12B. PP2BP4_StrongBA1
The NM_005063.5(SCD):āc.670A>Cā(p.Met224Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.412 in 1,613,390 control chromosomes in the GnomAD database, including 138,873 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_005063.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -11 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCD | NM_005063.5 | c.670A>C | p.Met224Leu | missense_variant | 5/6 | ENST00000370355.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCD | ENST00000370355.3 | c.670A>C | p.Met224Leu | missense_variant | 5/6 | 1 | NM_005063.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.402 AC: 61124AN: 151922Hom.: 12443 Cov.: 32
GnomAD3 exomes AF: 0.412 AC: 103405AN: 251106Hom.: 22140 AF XY: 0.401 AC XY: 54463AN XY: 135700
GnomAD4 exome AF: 0.413 AC: 602809AN: 1461350Hom.: 126419 Cov.: 43 AF XY: 0.408 AC XY: 296939AN XY: 727012
GnomAD4 genome AF: 0.402 AC: 61167AN: 152040Hom.: 12454 Cov.: 32 AF XY: 0.398 AC XY: 29569AN XY: 74308
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at