chr2-201492262-G-A
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_001168221.2(C2CD6):c.4079C>T(p.Pro1360Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000394 in 1,523,646 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001168221.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C2CD6 | NM_001168221.2 | c.4079C>T | p.Pro1360Leu | missense_variant | 15/16 | ENST00000439140.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C2CD6 | ENST00000439140.6 | c.4079C>T | p.Pro1360Leu | missense_variant | 15/16 | 1 | NM_001168221.2 | A2 | |
C2CD6 | ENST00000286195.7 | c.1581+3633C>T | intron_variant | 1 | P2 | ||||
C2CD6 | ENST00000439802.5 | c.*49+3633C>T | intron_variant | 2 | |||||
C2CD6 | ENST00000482942.1 | n.101-4360C>T | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152002Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000146 AC: 2AN: 1371644Hom.: 0 Cov.: 32 AF XY: 0.00000296 AC XY: 2AN XY: 676732
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152002Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74252
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 21, 2023 | The c.4079C>T (p.P1360L) alteration is located in exon 15 (coding exon 15) of the ALS2CR11 gene. This alteration results from a C to T substitution at nucleotide position 4079, causing the proline (P) at amino acid position 1360 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