chr3-46408395-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003965.5(CCRL2):c.316C>T(p.Leu106Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000929 in 1,614,098 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. L106I) has been classified as Uncertain significance.
Frequency
Consequence
NM_003965.5 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCRL2 | NM_003965.5 | c.316C>T | p.Leu106Phe | missense_variant | Exon 2 of 2 | ENST00000399036.4 | NP_003956.2 | |
CCRL2 | NM_001130910.2 | c.352C>T | p.Leu118Phe | missense_variant | Exon 2 of 2 | NP_001124382.1 | ||
CCRL2 | XM_011534208.2 | c.316C>T | p.Leu106Phe | missense_variant | Exon 3 of 3 | XP_011532510.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000591 AC: 9AN: 152232Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249462Hom.: 0 AF XY: 0.0000296 AC XY: 4AN XY: 135330
GnomAD4 exome AF: 0.0000965 AC: 141AN: 1461866Hom.: 0 Cov.: 34 AF XY: 0.000100 AC XY: 73AN XY: 727234
GnomAD4 genome AF: 0.0000591 AC: 9AN: 152232Hom.: 0 Cov.: 33 AF XY: 0.0000538 AC XY: 4AN XY: 74378
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at