chr2-201492363-C-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_001168221.2(C2CD6):c.3978G>C(p.Gln1326His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0104 in 1,534,982 control chromosomes in the GnomAD database, including 99 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/17 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Consequence
NM_001168221.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
C2CD6 | NM_001168221.2 | c.3978G>C | p.Gln1326His | missense_variant | 15/16 | ENST00000439140.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
C2CD6 | ENST00000439140.6 | c.3978G>C | p.Gln1326His | missense_variant | 15/16 | 1 | NM_001168221.2 | A2 | |
C2CD6 | ENST00000286195.7 | c.1581+3532G>C | intron_variant | 1 | P2 | ||||
C2CD6 | ENST00000439802.5 | c.*49+3532G>C | intron_variant | 2 | |||||
C2CD6 | ENST00000482942.1 | n.101-4461G>C | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00932 AC: 1417AN: 152062Hom.: 10 Cov.: 32
GnomAD3 exomes AF: 0.00834 AC: 1164AN: 139566Hom.: 3 AF XY: 0.00840 AC XY: 631AN XY: 75102
GnomAD4 exome AF: 0.0106 AC: 14609AN: 1382802Hom.: 89 Cov.: 32 AF XY: 0.0107 AC XY: 7300AN XY: 682400
GnomAD4 genome ? AF: 0.00931 AC: 1417AN: 152180Hom.: 10 Cov.: 32 AF XY: 0.00945 AC XY: 703AN XY: 74418
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2023 | C2CD6: BP4, BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at