chr12-9982082-T-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_138337.6(CLEC12A):c.594T>A(p.Asp198Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000487 in 1,601,654 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_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.594T>A | p.Asp198Glu | missense_variant | 5/6 | ENST00000304361.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC12A | ENST00000304361.9 | c.594T>A | p.Asp198Glu | missense_variant | 5/6 | 1 | NM_138337.6 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152098Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000320 AC: 8AN: 249940Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135184
GnomAD4 exome AF: 0.0000504 AC: 73AN: 1449556Hom.: 0 Cov.: 26 AF XY: 0.0000513 AC XY: 37AN XY: 721904
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152098Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74288
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 24, 2023 | The c.624T>A (p.D208E) alteration is located in exon 6 (coding exon 6) of the CLEC12A gene. This alteration results from a T to A substitution at nucleotide position 624, causing the aspartic acid (D) at amino acid position 208 to be replaced by a glutamic acid (E). 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