chr19-41577200-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001098506.4(CEACAM21):c.65C>T(p.Ala22Val) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000118 in 1,613,856 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001098506.4 missense, splice_region
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 | UniProt |
---|---|---|---|---|---|---|---|
CEACAM21 | NM_001098506.4 | c.65C>T | p.Ala22Val | missense_variant, splice_region_variant | 2/7 | ENST00000401445.4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM21 | ENST00000401445.4 | c.65C>T | p.Ala22Val | missense_variant, splice_region_variant | 2/7 | 1 | NM_001098506.4 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.000269 AC: 41AN: 152140Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250222Hom.: 0 AF XY: 0.0000958 AC XY: 13AN XY: 135708
GnomAD4 exome AF: 0.000103 AC: 150AN: 1461716Hom.: 0 Cov.: 33 AF XY: 0.000102 AC XY: 74AN XY: 727168
GnomAD4 genome ? AF: 0.000269 AC: 41AN: 152140Hom.: 0 Cov.: 32 AF XY: 0.000296 AC XY: 22AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 27, 2022 | The c.65C>T (p.A22V) alteration is located in exon 2 (coding exon 2) of the CEACAM21 gene. This alteration results from a C to T substitution at nucleotide position 65, causing the alanine (A) at amino acid position 22 to be replaced by a valine (V). 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