rs114645388
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_StrongBP6_Very_StrongBP7
The NM_001039213.4(CEACAM16):c.519C>T(p.Val173=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000143 in 1,589,278 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★).
Frequency
Genomes: 𝑓 0.00079 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000074 ( 0 hom. )
Consequence
CEACAM16
NM_001039213.4 synonymous
NM_001039213.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.37
Genes affected
CEACAM16 (HGNC:31948): (CEA cell adhesion molecule 16, tectorial membrane component) The protein encoded by this gene is a secreted glycoprotein that in mouse interacts with tectorial membrane proteins in the inner ear. The encoded adhesion protein is found in cochlear outer hair cells and appears to be important for proper hearing over an extended frequency range. Defects in this gene likely are a cause of non-syndromic autosomal dominant hearing loss. [provided by RefSeq, May 2012]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.78).
BP6
?
Variant 19-44704154-C-T is Benign according to our data. Variant chr19-44704154-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 227241.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BP7
?
Synonymous conserved (PhyloP=-2.37 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEACAM16 | NM_001039213.4 | c.519C>T | p.Val173= | synonymous_variant | 4/7 | ENST00000587331.7 | |
CEACAM16 | XM_017026795.2 | c.519C>T | p.Val173= | synonymous_variant | 3/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM16 | ENST00000587331.7 | c.519C>T | p.Val173= | synonymous_variant | 4/7 | 1 | NM_001039213.4 | P1 | |
CEACAM16-AS1 | ENST00000662585.1 | n.382-4977G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.000788 AC: 120AN: 152256Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000138 AC: 28AN: 203334Hom.: 0 AF XY: 0.0000991 AC XY: 11AN XY: 110944
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GnomAD4 exome AF: 0.0000745 AC: 107AN: 1436904Hom.: 0 Cov.: 32 AF XY: 0.0000617 AC XY: 44AN XY: 712974
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GnomAD4 genome ? AF: 0.000788 AC: 120AN: 152374Hom.: 0 Cov.: 32 AF XY: 0.000644 AC XY: 48AN XY: 74518
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ClinVar
Significance: Benign/Likely benign
Submissions summary: Benign:4
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 01, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 06, 2023 | - - |
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Laboratory for Molecular Medicine, Mass General Brigham Personalized Medicine | May 18, 2017 | p.Val173Val in exon 4 of CEACAM16: This variant is not expected to have clinical significance because it does not alter an amino acid residue and is not located within the splice consensus sequence, and it has been identified in 0.2% (44/19 532) of African chromosomes by the Genome Aggregation Database (gnomAD, http://g nomad.broadinstitute.org; dbSNP rs114645388). - |
CEACAM16-related disorder Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 10, 2019 | 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
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at