chr1-158356759-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_030893.4(CD1E):c.1030C>T(p.Pro344Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000208 in 1,613,752 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.1030C>T | p.Pro344Ser | missense_variant | 6/6 | ENST00000368167.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CD1E | ENST00000368167.8 | c.1030C>T | p.Pro344Ser | missense_variant | 6/6 | 1 | NM_030893.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 151966Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000188 AC: 47AN: 249550Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135400
GnomAD4 exome AF: 0.000210 AC: 307AN: 1461786Hom.: 0 Cov.: 32 AF XY: 0.000204 AC XY: 148AN XY: 727206
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 151966Hom.: 0 Cov.: 32 AF XY: 0.000135 AC XY: 10AN XY: 74222
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 17, 2023 | The c.1030C>T (p.P344S) alteration is located in exon 6 (coding exon 6) of the CD1E gene. This alteration results from a C to T substitution at nucleotide position 1030, causing the proline (P) at amino acid position 344 to be replaced by a serine (S). 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