3-46408383-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003965.5(CCRL2):āc.304A>Gā(p.Met102Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000015 in 1,461,878 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 (ā ).
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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CCRL2 | NM_003965.5 | c.304A>G | p.Met102Val | missense_variant | 2/2 | ENST00000399036.4 | |
CCRL2 | NM_001130910.2 | c.340A>G | p.Met114Val | missense_variant | 2/2 | ||
CCRL2 | XM_011534208.2 | c.304A>G | p.Met102Val | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CCRL2 | ENST00000399036.4 | c.304A>G | p.Met102Val | missense_variant | 2/2 | 1 | NM_003965.5 | P2 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000802 AC: 2AN: 249468Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135336
GnomAD4 exome AF: 0.0000150 AC: 22AN: 1461878Hom.: 0 Cov.: 34 AF XY: 0.00000825 AC XY: 6AN XY: 727242
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 24, 2023 | The c.340A>G (p.M114V) alteration is located in exon 2 (coding exon 2) of the CCRL2 gene. This alteration results from a A to G substitution at nucleotide position 340, causing the methionine (M) at amino acid position 114 to be replaced by a valine (V). 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