rs6654021
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_001037540.3(SCML1):c.-117+208A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.154 in 111,037 control chromosomes in the GnomAD database, including 2,945 homozygotes. There are 4,508 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001037540.3 intron
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 |
---|---|---|---|---|---|---|---|
SCML1 | NM_001037540.3 | c.-117+208A>G | intron_variant | ENST00000380041.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCML1 | ENST00000380041.8 | c.-117+208A>G | intron_variant | 5 | NM_001037540.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.154 AC: 17055AN: 110960Hom.: 2944 Cov.: 22 AF XY: 0.134 AC XY: 4468AN XY: 33222
GnomAD4 exome AF: 0.0455 AC: 1AN: 22Hom.: 0 Cov.: 0 AF XY: 0.0714 AC XY: 1AN XY: 14
GnomAD4 genome ? AF: 0.154 AC: 17098AN: 111015Hom.: 2945 Cov.: 22 AF XY: 0.135 AC XY: 4507AN XY: 33287
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at