3-46408713-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP3_Moderate
The NM_003965.5(CCRL2):c.634C>T(p.Pro212Ser) variant causes a missense change. The variant allele was found at a frequency of 0.0000527 in 1,613,988 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar 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 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CCRL2 | NM_003965.5 | c.634C>T | p.Pro212Ser | missense_variant | Exon 2 of 2 | ENST00000399036.4 | NP_003956.2 | |
CCRL2 | NM_001130910.2 | c.670C>T | p.Pro224Ser | missense_variant | Exon 2 of 2 | NP_001124382.1 | ||
CCRL2 | XM_011534208.2 | c.634C>T | p.Pro212Ser | missense_variant | Exon 3 of 3 | XP_011532510.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152170Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249478Hom.: 0 AF XY: 0.0000443 AC XY: 6AN XY: 135354
GnomAD4 exome AF: 0.0000554 AC: 81AN: 1461818Hom.: 0 Cov.: 34 AF XY: 0.0000523 AC XY: 38AN XY: 727228
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152170Hom.: 0 Cov.: 33 AF XY: 0.0000269 AC XY: 2AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.670C>T (p.P224S) alteration is located in exon 2 (coding exon 2) of the CCRL2 gene. This alteration results from a C to T substitution at nucleotide position 670, causing the proline (P) at amino acid position 224 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