12-9979447-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138337.6(CLEC12A):āc.302A>Gā(p.Asn101Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,426 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 (ā ).
Frequency
Consequence
NM_138337.6 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 |
---|---|---|---|---|---|---|---|
CLEC12A | NM_138337.6 | c.302A>G | p.Asn101Ser | missense_variant | 3/6 | ENST00000304361.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC12A | ENST00000304361.9 | c.302A>G | p.Asn101Ser | missense_variant | 3/6 | 1 | NM_138337.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152224Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000600 AC: 15AN: 249948Hom.: 0 AF XY: 0.0000222 AC XY: 3AN XY: 135152
GnomAD4 exome AF: 0.0000178 AC: 26AN: 1461084Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 726842
GnomAD4 genome AF: 0.000197 AC: 30AN: 152342Hom.: 0 Cov.: 32 AF XY: 0.000174 AC XY: 13AN XY: 74502
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 11, 2023 | The c.332A>G (p.N111S) alteration is located in exon 4 (coding exon 4) of the CLEC12A gene. This alteration results from a A to G substitution at nucleotide position 332, causing the asparagine (N) at amino acid position 111 to be replaced by a serine (S). 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