chr19-44522840-C-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001102597.3(CEACAM20):c.545G>T(p.Gly182Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000497 in 1,611,162 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 31)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
CEACAM20
NM_001102597.3 missense
NM_001102597.3 missense
Scores
2
2
5
Clinical Significance
Conservation
PhyloP100: 0.247
Genes affected
CEACAM20 (HGNC:24879): (CEA cell adhesion molecule 20) Predicted to be involved in positive regulation of cytokine production. Predicted to act upstream of or within response to bacterium. Predicted to be located in apical plasma membrane and microvillus membrane. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEACAM20 | NM_001102597.3 | c.545G>T | p.Gly182Val | missense_variant | 4/12 | ENST00000614924.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM20 | ENST00000614924.5 | c.545G>T | p.Gly182Val | missense_variant | 4/12 | 1 | NM_001102597.3 | A2 |
Frequencies
GnomAD3 genomes ? AF: 0.00000658 AC: 1AN: 152090Hom.: 0 Cov.: 31
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GnomAD3 exomes AF: 0.00000410 AC: 1AN: 243956Hom.: 0 AF XY: 0.00000757 AC XY: 1AN XY: 132172
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GnomAD4 exome AF: 0.00000480 AC: 7AN: 1459072Hom.: 0 Cov.: 32 AF XY: 0.00000276 AC XY: 2AN XY: 725512
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GnomAD4 genome ? AF: 0.00000658 AC: 1AN: 152090Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74314
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 30, 2023 | The c.545G>T (p.G182V) alteration is located in exon 4 (coding exon 4) of the CEACAM20 gene. This alteration results from a G to T substitution at nucleotide position 545, causing the glycine (G) at amino acid position 182 to be replaced by a valine (V). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
FATHMM_MKL
Benign
N
LIST_S2
Benign
T;T;T;T;T;T
MetaRNN
Uncertain
D;D;D;D;D;D
PrimateAI
Benign
T
Sift4G
Pathogenic
D;D;D;D;D;D
Polyphen
1.0
.;.;.;D;.;.
Vest4
MVP
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at