11-117428430-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 3P and 2B. PM2PP2BP4_Moderate
The NM_020693.4(DSCAML1):c.6060G>A(p.Met2020Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000215 in 1,396,682 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_020693.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
DSCAML1 | NM_020693.4 | c.6060G>A | p.Met2020Ile | missense_variant | 33/33 | ENST00000651296.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
DSCAML1 | ENST00000651296.2 | c.6060G>A | p.Met2020Ile | missense_variant | 33/33 | NM_020693.4 | |||
DSCAML1 | ENST00000321322.6 | c.6240G>A | p.Met2080Ile | missense_variant | 33/33 | 1 | P1 | ||
DSCAML1 | ENST00000651172.1 | c.6240G>A | p.Met2080Ile | missense_variant | 33/33 | P1 | |||
DSCAML1 | ENST00000527706.5 | c.5430G>A | p.Met1810Ile | missense_variant | 31/31 | 5 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome AF: 0.00000215 AC: 3AN: 1396682Hom.: 0 Cov.: 33 AF XY: 0.00000145 AC XY: 1AN XY: 689978
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Jan 07, 2024 | This sequence change replaces methionine, which is neutral and non-polar, with isoleucine, which is neutral and non-polar, at codon 2080 of the DSCAML1 protein (p.Met2080Ile). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with DSCAML1-related conditions. ClinVar contains an entry for this variant (Variation ID: 2183570). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at