chr2-3643958-A-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_024027.5(COLEC11):āc.656A>Gā(p.His219Arg) variant causes a missense change. The variant allele was found at a frequency of 0.0685 in 1,613,746 control chromosomes in the GnomAD database, including 19,382 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_024027.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLEC11 | NM_024027.5 | c.656A>G | p.His219Arg | missense_variant | 7/7 | ENST00000349077.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLEC11 | ENST00000349077.9 | c.656A>G | p.His219Arg | missense_variant | 7/7 | 1 | NM_024027.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.215 AC: 32710AN: 151850Hom.: 9482 Cov.: 34
GnomAD3 exomes AF: 0.0845 AC: 21235AN: 251312Hom.: 4159 AF XY: 0.0749 AC XY: 10176AN XY: 135868
GnomAD4 exome AF: 0.0531 AC: 77681AN: 1461780Hom.: 9862 Cov.: 32 AF XY: 0.0528 AC XY: 38427AN XY: 727196
GnomAD4 genome AF: 0.216 AC: 32804AN: 151966Hom.: 9520 Cov.: 34 AF XY: 0.210 AC XY: 15594AN XY: 74258
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at