19-44703362-T-C
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_001039213.4(CEACAM16):āc.51T>Cā(p.Asn17Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00241 in 1,609,440 control chromosomes in the GnomAD database, including 117 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ā ).
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.51T>C | p.Asn17Asn | synonymous_variant | Exon 3 of 7 | ENST00000587331.7 | NP_001034302.2 | |
CEACAM16 | XM_017026795.2 | c.51T>C | p.Asn17Asn | synonymous_variant | Exon 2 of 5 | XP_016882284.1 | ||
CEACAM16-AS1 | NR_186815.1 | n.348-4185A>G | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00113 AC: 172AN: 152104Hom.: 5 Cov.: 32
GnomAD3 exomes AF: 0.00545 AC: 1342AN: 246300Hom.: 45 AF XY: 0.00742 AC XY: 993AN XY: 133868
GnomAD4 exome AF: 0.00254 AC: 3699AN: 1457218Hom.: 112 Cov.: 32 AF XY: 0.00374 AC XY: 2711AN XY: 723966
GnomAD4 genome AF: 0.00114 AC: 173AN: 152222Hom.: 5 Cov.: 32 AF XY: 0.00175 AC XY: 130AN XY: 74456
ClinVar
Submissions by phenotype
not specified Benign:3
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
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p.Asn17Asn in exon 3 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. It has been identified in 699/15188 (4.6%) of South Asian chromosomes including 24 homozygotes by the Exome Aggregation Co nsortium (ExAC, http://exac.broadinstitute.org; dbSNP rs202230938). -
not provided Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at