chr19-41585852-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001098506.4(CEACAM21):c.863C>T(p.Ser288Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000973 in 1,612,936 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098506.4 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEACAM21 | NM_001098506.4 | c.863C>T | p.Ser288Phe | missense_variant | 6/7 | ENST00000401445.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM21 | ENST00000401445.4 | c.863C>T | p.Ser288Phe | missense_variant | 6/7 | 1 | NM_001098506.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 247178Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134036
GnomAD4 exome AF: 0.000103 AC: 150AN: 1460758Hom.: 1 Cov.: 31 AF XY: 0.0000936 AC XY: 68AN XY: 726496
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152178Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74344
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Nov 18, 2022 | The c.863C>T (p.S288F) alteration is located in exon 6 (coding exon 6) of the CEACAM21 gene. This alteration results from a C to T substitution at nucleotide position 863, causing the serine (S) at amino acid position 288 to be replaced by a phenylalanine (F). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at