2-201492266-T-C
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 3P and 4B. PM2PP2BP4_Strong
The NM_001168221.2(C2CD6):c.4075A>G(p.Ile1359Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000157 in 1,531,830 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/18 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.4075A>G | p.Ile1359Val | missense_variant | 15/16 | ENST00000439140.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C2CD6 | ENST00000439140.6 | c.4075A>G | p.Ile1359Val | missense_variant | 15/16 | 1 | NM_001168221.2 | A2 | |
C2CD6 | ENST00000286195.7 | c.1581+3629A>G | intron_variant | 1 | P2 | ||||
C2CD6 | ENST00000439802.5 | c.*49+3629A>G | intron_variant | 2 | |||||
C2CD6 | ENST00000482942.1 | n.101-4364A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000507 AC: 7AN: 137940Hom.: 0 AF XY: 0.0000406 AC XY: 3AN XY: 73978
GnomAD4 exome AF: 0.0000145 AC: 20AN: 1379668Hom.: 0 Cov.: 32 AF XY: 0.0000147 AC XY: 10AN XY: 680942
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152162Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 25, 2022 | The c.4075A>G (p.I1359V) alteration is located in exon 15 (coding exon 15) of the ALS2CR11 gene. This alteration results from a A to G substitution at nucleotide position 4075, causing the isoleucine (I) at amino acid position 1359 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