rs59028589
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 1P and 0B. PP3
The NM_001039213.4(CEACAM16):c.539C>A(p.Ser180Tyr) variant causes a missense change. The variant allele was found at a frequency of 0.0000038 in 1,578,212 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S180F) has been classified as Benign.
Frequency
Consequence
NM_001039213.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEACAM16 | NM_001039213.4 | c.539C>A | p.Ser180Tyr | missense_variant | 4/7 | ENST00000587331.7 | |
CEACAM16 | XM_017026795.2 | c.539C>A | p.Ser180Tyr | missense_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM16 | ENST00000587331.7 | c.539C>A | p.Ser180Tyr | missense_variant | 4/7 | 1 | NM_001039213.4 | P1 | |
CEACAM16-AS1 | ENST00000662585.1 | n.382-4997G>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152252Hom.: 0 Cov.: 32
GnomAD4 exome AF: 0.00000281 AC: 4AN: 1425842Hom.: 0 Cov.: 32 AF XY: 0.00000142 AC XY: 1AN XY: 706174
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152370Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74510
ClinVar
Not reported inComputational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at