chr12-10127819-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_197947.3(CLEC7A):c.130C>T(p.Arg44Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,568,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R44H) has been classified as Uncertain significance.
Frequency
Consequence
NM_197947.3 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CLEC7A | NM_197947.3 | c.130C>T | p.Arg44Cys | missense_variant | 2/6 | ENST00000304084.13 | |
LOC105369655 | XR_007063208.1 | n.182-3262G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC7A | ENST00000304084.13 | c.130C>T | p.Arg44Cys | missense_variant | 2/6 | 1 | NM_197947.3 | P4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000724 AC: 11AN: 152006Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000222 AC: 4AN: 180218Hom.: 0 AF XY: 0.0000211 AC XY: 2AN XY: 94938
GnomAD4 exome AF: 0.0000184 AC: 26AN: 1416646Hom.: 0 Cov.: 30 AF XY: 0.0000129 AC XY: 9AN XY: 700098
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152124Hom.: 0 Cov.: 31 AF XY: 0.0000672 AC XY: 5AN XY: 74370
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.130C>T (p.R44C) alteration is located in exon 2 (coding exon 2) of the CLEC7A gene. This alteration results from a C to T substitution at nucleotide position 130, causing the arginine (R) at amino acid position 44 to be replaced by a cysteine (C). 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