1-158356871-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_030893.4(CD1E):c.1142A>G(p.Lys381Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000204 in 1,613,974 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_030893.4 missense
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 |
---|---|---|---|---|---|---|---|
CD1E | NM_030893.4 | c.1142A>G | p.Lys381Arg | missense_variant | 6/6 | ENST00000368167.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD1E | ENST00000368167.8 | c.1142A>G | p.Lys381Arg | missense_variant | 6/6 | 1 | NM_030893.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000394 AC: 6AN: 152126Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000401 AC: 10AN: 249538Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135386
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461848Hom.: 0 Cov.: 32 AF XY: 0.0000179 AC XY: 13AN XY: 727222
GnomAD4 genome ? AF: 0.0000394 AC: 6AN: 152126Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74304
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 06, 2023 | The c.1142A>G (p.K381R) alteration is located in exon 6 (coding exon 6) of the CD1E gene. This alteration results from a A to G substitution at nucleotide position 1142, causing the lysine (K) at amino acid position 381 to be replaced by an arginine (R). 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