chr2-3613345-C-T
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 2P and 12B. PM2BP4_StrongBP6_Very_Strong
The ENST00000236693.11(COLEC11):c.77C>T(p.Pro26Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000646 in 1,609,598 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/15 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
ENST00000236693.11 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -10 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
COLEC11 | NM_024027.5 | c.165C>T | p.Pro55= | synonymous_variant | 3/7 | ENST00000349077.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
COLEC11 | ENST00000349077.9 | c.165C>T | p.Pro55= | synonymous_variant | 3/7 | 1 | NM_024027.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000473 AC: 72AN: 152180Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000360 AC: 86AN: 238578Hom.: 0 AF XY: 0.000341 AC XY: 44AN XY: 129084
GnomAD4 exome AF: 0.000664 AC: 968AN: 1457418Hom.: 1 Cov.: 32 AF XY: 0.000640 AC XY: 464AN XY: 724446
GnomAD4 genome ? AF: 0.000473 AC: 72AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74336
ClinVar
Submissions by phenotype
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 31, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at