chr16-10972947-A-C
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_015226.3(CLEC16A):āc.614A>Cā(p.Gln205Pro) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00000125 in 1,601,474 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q205E) has been classified as Uncertain significance.
Frequency
Consequence
NM_015226.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC16A | NM_015226.3 | c.614A>C | p.Gln205Pro | missense_variant | 7/24 | ENST00000409790.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC16A | ENST00000409790.6 | c.614A>C | p.Gln205Pro | missense_variant | 7/24 | 5 | NM_015226.3 | A1 | |
CLEC16A | ENST00000409552.4 | c.608A>C | p.Gln203Pro | missense_variant | 6/21 | 1 | |||
CLEC16A | ENST00000703130.1 | c.608A>C | p.Gln203Pro | missense_variant | 6/23 | P4 | |||
CLEC16A | ENST00000494853.1 | n.89A>C | non_coding_transcript_exon_variant | 2/8 | 3 |
Frequencies
GnomAD3 genomes AF: 0.00000671 AC: 1AN: 149046Hom.: 0 Cov.: 31
GnomAD4 exome AF: 6.89e-7 AC: 1AN: 1452428Hom.: 0 Cov.: 32 AF XY: 0.00000138 AC XY: 1AN XY: 722056
GnomAD4 genome AF: 0.00000671 AC: 1AN: 149046Hom.: 0 Cov.: 31 AF XY: 0.0000138 AC XY: 1AN XY: 72388
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 12, 2021 | The c.614A>C (p.Q205P) alteration is located in exon 7 (coding exon 7) of the CLEC16A gene. This alteration results from a A to C substitution at nucleotide position 614, causing the glutamine (Q) at amino acid position 205 to be replaced by a proline (P). 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