19-44710480-C-T
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_001039213.4(CEACAM16):c.1268-16C>T variant causes a splice polypyrimidine tract, intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0457 in 1,611,444 control chromosomes in the GnomAD database, including 1,854 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.042 ( 169 hom., cov: 33)
Exomes 𝑓: 0.046 ( 1685 hom. )
Consequence
CEACAM16
NM_001039213.4 splice_polypyrimidine_tract, intron
NM_001039213.4 splice_polypyrimidine_tract, intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.02
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 -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.8).
BP6
Variant 19-44710480-C-T is Benign according to our data. Variant chr19-44710480-C-T is described in ClinVar as [Benign]. Clinvar id is 257226.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0603 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEACAM16 | NM_001039213.4 | c.1268-16C>T | splice_polypyrimidine_tract_variant, intron_variant | ENST00000587331.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM16 | ENST00000587331.7 | c.1268-16C>T | splice_polypyrimidine_tract_variant, intron_variant | 1 | NM_001039213.4 | P1 | |||
CEACAM16-AS1 | ENST00000662585.1 | n.382-11303G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.0418 AC: 6357AN: 152130Hom.: 169 Cov.: 33
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GnomAD3 exomes AF: 0.0428 AC: 10575AN: 247160Hom.: 278 AF XY: 0.0458 AC XY: 6146AN XY: 134118
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GnomAD4 exome AF: 0.0461 AC: 67297AN: 1459196Hom.: 1685 Cov.: 31 AF XY: 0.0474 AC XY: 34378AN XY: 725754
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GnomAD4 genome AF: 0.0418 AC: 6359AN: 152248Hom.: 169 Cov.: 33 AF XY: 0.0420 AC XY: 3126AN XY: 74432
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ClinVar
Significance: Benign
Submissions summary: Benign:3
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 31, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Jun 22, 2018 | - - |
not specified Benign:1
Benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at