19-44703393-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001039213.4(CEACAM16):āc.82C>Gā(p.Pro28Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000155 in 1,613,528 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ā ).
Frequency
Consequence
NM_001039213.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEACAM16 | NM_001039213.4 | c.82C>G | p.Pro28Ala | missense_variant | Exon 3 of 7 | ENST00000587331.7 | NP_001034302.2 | |
CEACAM16 | XM_017026795.2 | c.82C>G | p.Pro28Ala | missense_variant | Exon 2 of 5 | XP_016882284.1 | ||
CEACAM16-AS1 | NR_186815.1 | n.348-4216G>C | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000197 AC: 3AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000121 AC: 3AN: 247416Hom.: 0 AF XY: 0.00000744 AC XY: 1AN XY: 134422
GnomAD4 exome AF: 0.0000151 AC: 22AN: 1461322Hom.: 0 Cov.: 32 AF XY: 0.0000193 AC XY: 14AN XY: 726956
GnomAD4 genome AF: 0.0000197 AC: 3AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74368
ClinVar
Submissions by phenotype
not provided Uncertain:2
In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge -
This sequence change replaces proline, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 28 of the CEACAM16 protein (p.Pro28Ala). This variant is present in population databases (rs746286359, gnomAD 0.003%). This variant has not been reported in the literature in individuals affected with CEACAM16-related conditions. ClinVar contains an entry for this variant (Variation ID: 1496986). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt CEACAM16 protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at