NM_001039213.4:c.738G>A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001039213.4(CEACAM16):c.738G>A(p.Thr246Thr) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00407 in 1,613,772 control chromosomes in the GnomAD database, including 21 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Consequence
NM_001039213.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEACAM16 | NM_001039213.4 | c.738G>A | p.Thr246Thr | synonymous_variant | Exon 5 of 7 | ENST00000587331.7 | NP_001034302.2 | |
CEACAM16 | XM_017026795.2 | c.738G>A | p.Thr246Thr | synonymous_variant | Exon 4 of 5 | XP_016882284.1 | ||
CEACAM16-AS1 | NR_186815.1 | n.348-6489C>T | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00281 AC: 428AN: 152152Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00350 AC: 870AN: 248464Hom.: 7 AF XY: 0.00349 AC XY: 471AN XY: 134810
GnomAD4 exome AF: 0.00421 AC: 6148AN: 1461502Hom.: 20 Cov.: 32 AF XY: 0.00409 AC XY: 2970AN XY: 727014
GnomAD4 genome AF: 0.00281 AC: 428AN: 152270Hom.: 1 Cov.: 32 AF XY: 0.00282 AC XY: 210AN XY: 74462
ClinVar
Submissions by phenotype
not provided Benign:5
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CEACAM16: BP4, BP7, BS2 -
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not specified Benign:2
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Thr246Thr in exon 5 of CEACAM16: This variant is not expected to have clinical s ignificance because it does not alter an amino acid residue and is not located w ithin the splice consensus sequence. It has been identified in 0.4% (32/8468) of European American chromosomes from a broad population by the NHLBI Exome Sequen cing Project (http://evs.gs.washington.edu/EVS). -
CEACAM16-related disorder Benign:1
This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at