19-44703406-G-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_001039213.4(CEACAM16):c.95G>T(p.Ser32Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00161 in 1,613,786 control chromosomes in the GnomAD database, including 8 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin ClinVar. Synonymous variant affecting the same amino acid position (i.e. S32S) has been classified as Likely benign.
Frequency
Consequence
NM_001039213.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEACAM16 | NM_001039213.4 | c.95G>T | p.Ser32Ile | missense_variant | 3/7 | ENST00000587331.7 | |
CEACAM16 | XM_017026795.2 | c.95G>T | p.Ser32Ile | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM16 | ENST00000587331.7 | c.95G>T | p.Ser32Ile | missense_variant | 3/7 | 1 | NM_001039213.4 | P1 | |
CEACAM16-AS1 | ENST00000662585.1 | n.382-4229C>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00183 AC: 279AN: 152202Hom.: 3 Cov.: 32
GnomAD3 exomes AF: 0.00196 AC: 488AN: 248360Hom.: 3 AF XY: 0.00168 AC XY: 226AN XY: 134848
GnomAD4 exome AF: 0.00159 AC: 2327AN: 1461466Hom.: 6 Cov.: 32 AF XY: 0.00153 AC XY: 1116AN XY: 727034
GnomAD4 genome AF: 0.00182 AC: 277AN: 152320Hom.: 2 Cov.: 32 AF XY: 0.00177 AC XY: 132AN XY: 74490
ClinVar
Submissions by phenotype
not provided Benign:3
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 30, 2020 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Aug 01, 2023 | CEACAM16: BP4, BS2 - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 14, 2015 | p.Ser32Ile in exon 3 of CEACAM16: This variant is not expected to have clinical significance because it has been identified in 0.9% (109/11536) of Latino chromo somes including 3 homozygotes by the Exome Aggregation Consortium (ExAC, http:// exac.broadinstitute.org; dbSNP rs186687142). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at