1-158356768-G-C
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030893.4(CD1E):c.1039G>C(p.Val347Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000242 in 1,612,348 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 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 Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CD1E | NM_030893.4 | c.1039G>C | p.Val347Leu | missense_variant | 6/6 | ENST00000368167.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD1E | ENST00000368167.8 | c.1039G>C | p.Val347Leu | missense_variant | 6/6 | 1 | NM_030893.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000193 AC: 29AN: 150418Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000481 AC: 12AN: 249550Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135402
GnomAD4 exome AF: 0.00000684 AC: 10AN: 1461814Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 2AN XY: 727222
GnomAD4 genome ? AF: 0.000193 AC: 29AN: 150534Hom.: 0 Cov.: 32 AF XY: 0.000150 AC XY: 11AN XY: 73336
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2022 | The c.1039G>C (p.V347L) alteration is located in exon 6 (coding exon 6) of the CD1E gene. This alteration results from a G to C substitution at nucleotide position 1039, causing the valine (V) at amino acid position 347 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