16-11020241-C-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_015226.3(CLEC16A):c.1352C>G(p.Ala451Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000304 in 1,613,790 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_015226.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC16A | NM_015226.3 | c.1352C>G | p.Ala451Gly | missense_variant | 12/24 | ENST00000409790.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC16A | ENST00000409790.6 | c.1352C>G | p.Ala451Gly | missense_variant | 12/24 | 5 | NM_015226.3 | A1 | |
CLEC16A | ENST00000409552.4 | c.1298C>G | p.Ala433Gly | missense_variant | 11/21 | 1 | |||
CLEC16A | ENST00000703130.1 | c.1346C>G | p.Ala449Gly | missense_variant | 11/23 | P4 | |||
CLEC16A | ENST00000494853.1 | n.827C>G | non_coding_transcript_exon_variant | 7/8 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.0000985 AC: 15AN: 152250Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000404 AC: 10AN: 247710Hom.: 0 AF XY: 0.0000223 AC XY: 3AN XY: 134598
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461422Hom.: 0 Cov.: 31 AF XY: 0.0000193 AC XY: 14AN XY: 727008
GnomAD4 genome ? AF: 0.0000984 AC: 15AN: 152368Hom.: 0 Cov.: 33 AF XY: 0.0000537 AC XY: 4AN XY: 74514
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 24, 2023 | The c.1352C>G (p.A451G) alteration is located in exon 12 (coding exon 12) of the CLEC16A gene. This alteration results from a C to G substitution at nucleotide position 1352, causing the alanine (A) at amino acid position 451 to be replaced by a glycine (G). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at