chr19-41577397-G-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001098506.4(CEACAM21):c.262G>A(p.Val88Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000936 in 1,614,034 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/18 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
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEACAM21 | NM_001098506.4 | c.262G>A | p.Val88Ile | missense_variant | 2/7 | ENST00000401445.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM21 | ENST00000401445.4 | c.262G>A | p.Val88Ile | missense_variant | 2/7 | 1 | NM_001098506.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000447 AC: 68AN: 152028Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000919 AC: 23AN: 250230Hom.: 0 AF XY: 0.0000737 AC XY: 10AN XY: 135704
GnomAD4 exome AF: 0.0000568 AC: 83AN: 1461888Hom.: 0 Cov.: 34 AF XY: 0.0000633 AC XY: 46AN XY: 727248
GnomAD4 genome ? AF: 0.000447 AC: 68AN: 152146Hom.: 0 Cov.: 32 AF XY: 0.000350 AC XY: 26AN XY: 74380
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.262G>A (p.V88I) alteration is located in exon 2 (coding exon 2) of the CEACAM21 gene. This alteration results from a G to A substitution at nucleotide position 262, causing the valine (V) at amino acid position 88 to be replaced by an isoleucine (I). 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