3-47413944-G-C
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_012235.4(SCAP):c.3750C>G(p.Ile1250Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000868 in 1,613,188 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012235.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SCAP | NM_012235.4 | c.3750C>G | p.Ile1250Met | missense_variant | 23/23 | ENST00000265565.10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SCAP | ENST00000265565.10 | c.3750C>G | p.Ile1250Met | missense_variant | 23/23 | 1 | NM_012235.4 | P1 | |
SCAP | ENST00000648151.1 | c.3750C>G | p.Ile1250Met | missense_variant | 24/24 | P1 | |||
SCAP | ENST00000320017.10 | c.*2464C>G | 3_prime_UTR_variant, NMD_transcript_variant | 18/18 | 2 | ||||
SCAP | ENST00000441517.6 | c.*2896C>G | 3_prime_UTR_variant, NMD_transcript_variant | 20/20 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251252Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135820
GnomAD4 exome AF: 0.00000890 AC: 13AN: 1461008Hom.: 0 Cov.: 32 AF XY: 0.0000110 AC XY: 8AN XY: 726812
GnomAD4 genome ? AF: 0.00000657 AC: 1AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74340
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 11, 2022 | The c.3750C>G (p.I1250M) alteration is located in exon 23 (coding exon 22) of the SCAP gene. This alteration results from a C to G substitution at nucleotide position 3750, causing the isoleucine (I) at amino acid position 1250 to be replaced by a methionine (M). 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