19-44708169-G-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_001039213.4(CEACAM16):c.1249G>T(p.Val417Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000159 in 1,576,434 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039213.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEACAM16 | NM_001039213.4 | c.1249G>T | p.Val417Leu | missense_variant | 6/7 | ENST00000587331.7 | NP_001034302.2 | |
CEACAM16 | XM_017026795.2 | c.1249G>T | p.Val417Leu | missense_variant | 5/5 | XP_016882284.1 | ||
CEACAM16-AS1 | NR_186815.1 | n.348-8992C>A | intron_variant |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152260Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.00000904 AC: 2AN: 221314Hom.: 0 AF XY: 0.00000833 AC XY: 1AN XY: 120084
GnomAD4 exome AF: 0.0000169 AC: 24AN: 1424174Hom.: 0 Cov.: 34 AF XY: 0.0000185 AC XY: 13AN XY: 701314
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152260Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74394
ClinVar
Submissions by phenotype
not provided Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 10, 2024 | Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at