19-41756789-G-A
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Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_002483.7(CEACAM6):c.254G>A(p.Gly85Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0047 in 1,613,966 control chromosomes in the GnomAD database, including 276 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.024 ( 163 hom., cov: 31)
Exomes 𝑓: 0.0027 ( 113 hom. )
Consequence
CEACAM6
NM_002483.7 missense
NM_002483.7 missense
Scores
15
Clinical Significance
Conservation
PhyloP100: -3.07
Genes affected
CEACAM6 (HGNC:1818): (CEA cell adhesion molecule 6) This gene encodes a protein that belongs to the carcinoembryonic antigen (CEA) family whose members are glycosyl phosphatidyl inositol (GPI) anchored cell surface glycoproteins. Members of this family play a role in cell adhesion and are widely used as tumor markers in serum immunoassay determinations of carcinoma. This gene affects the sensitivity of tumor cells to adenovirus infection. The protein encoded by this gene acts as a receptor for adherent-invasive E. coli adhesion to the surface of ileal epithelial cells in patients with Crohn's disease. This gene is clustered with genes and pseudogenes of the cell adhesion molecules subgroup of the CEA family on chromosome 19. [provided by RefSeq, Apr 2014]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (MetaRNN=0.0019599497).
BP6
Variant 19-41756789-G-A is Benign according to our data. Variant chr19-41756789-G-A is described in ClinVar as [Benign]. Clinvar id is 782649.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0804 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CEACAM6 | NM_002483.7 | c.254G>A | p.Gly85Glu | missense_variant | 2/6 | ENST00000199764.7 | |
LOC112268252 | XR_002958447.2 | n.1628C>T | non_coding_transcript_exon_variant | 2/2 | |||
CEACAM6 | XM_011526990.3 | c.254G>A | p.Gly85Glu | missense_variant | 2/5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CEACAM6 | ENST00000199764.7 | c.254G>A | p.Gly85Glu | missense_variant | 2/6 | 1 | NM_002483.7 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0238 AC: 3612AN: 151962Hom.: 160 Cov.: 31
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GnomAD3 exomes AF: 0.00701 AC: 1764AN: 251474Hom.: 76 AF XY: 0.00512 AC XY: 696AN XY: 135910
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GnomAD4 exome AF: 0.00270 AC: 3942AN: 1461886Hom.: 113 Cov.: 33 AF XY: 0.00236 AC XY: 1714AN XY: 727246
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GnomAD4 genome AF: 0.0239 AC: 3638AN: 152080Hom.: 163 Cov.: 31 AF XY: 0.0227 AC XY: 1687AN XY: 74364
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 28, 2017 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MetaRNN
Benign
T
MetaSVM
Benign
T
MutationTaster
Benign
N
PrimateAI
Benign
T
PROVEAN
Benign
N
REVEL
Benign
Sift
Benign
T
Sift4G
Benign
T
Vest4
MVP
MPC
ClinPred
T
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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