chr1-41075449-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001394311.1(SCMH1):c.748G>T(p.Val250Leu) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000868 in 1,613,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. 1/1 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001394311.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCMH1 | NM_001394311.1 | c.748G>T | p.Val250Leu | missense_variant, splice_region_variant | 9/16 | ENST00000695335.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCMH1 | ENST00000695335.1 | c.748G>T | p.Val250Leu | missense_variant, splice_region_variant | 9/16 | NM_001394311.1 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152076Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251216Hom.: 0 AF XY: 0.0000221 AC XY: 3AN XY: 135770
GnomAD4 exome AF: 0.0000883 AC: 129AN: 1460924Hom.: 0 Cov.: 31 AF XY: 0.0000784 AC XY: 57AN XY: 726850
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152076Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74276
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2022 | The c.718G>T (p.V240L) alteration is located in exon 9 (coding exon 6) of the SCMH1 gene. This alteration results from a G to T substitution at nucleotide position 718, causing the valine (V) at amino acid position 240 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at