19-44703372-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 0P and 0B.
The NM_001039213.4(CEACAM16):c.61G>A(p.Glu21Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000311 in 1,610,270 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001039213.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CEACAM16 | NM_001039213.4 | c.61G>A | p.Glu21Lys | missense_variant | Exon 3 of 7 | ENST00000587331.7 | NP_001034302.2 | |
CEACAM16 | XM_017026795.2 | c.61G>A | p.Glu21Lys | missense_variant | Exon 2 of 5 | XP_016882284.1 | ||
CEACAM16-AS1 | NR_186815.1 | n.348-4195C>T | intron_variant | Intron 1 of 1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152088Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000243 AC: 6AN: 246766Hom.: 0 AF XY: 0.0000224 AC XY: 3AN XY: 134032
GnomAD4 exome AF: 0.0000309 AC: 45AN: 1458182Hom.: 0 Cov.: 32 AF XY: 0.0000290 AC XY: 21AN XY: 724610
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152088Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
The p.Glu21Lys variant in CEACAM16 has not been previously reported in individua ls with hearing loss, but has been identified in 7/124532 European chromosomes b y the Genome Aggregation Database (gnomAD, http://gnomad.broadinstitute.org/; db SNP rs368296153). Although this variant has been seen in the general population, its frequency is not high enough to rule out a pathogenic role. Computational p rediction tools and conservation analysis do not provide strong support for or a gainst an impact to the protein. In summary, the clinical significance of the p. Glu21Lys variant is uncertain. ACMG/AMP Criteria applied: none. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at