17-7076919-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001330070.2(CLEC10A):c.253G>A(p.Ala85Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,874 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001330070.2 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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CLEC10A | NM_001330070.2 | c.253G>A | p.Ala85Thr | missense_variant | 4/9 | ENST00000416562.7 | NP_001316999.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CLEC10A | ENST00000416562.7 | c.253G>A | p.Ala85Thr | missense_variant | 4/9 | 5 | NM_001330070.2 | ENSP00000414938 | A2 | |
CLEC10A | ENST00000254868.8 | c.253G>A | p.Ala85Thr | missense_variant | 4/9 | 1 | ENSP00000254868 | |||
CLEC10A | ENST00000571664.1 | c.253G>A | p.Ala85Thr | missense_variant | 4/9 | 1 | ENSP00000460252 | P4 | ||
CLEC10A | ENST00000576617.5 | c.253G>A | p.Ala85Thr | missense_variant | 4/7 | 1 | ENSP00000458728 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151994Hom.: 0 Cov.: 28
GnomAD3 exomes AF: 0.0000835 AC: 21AN: 251484Hom.: 0 AF XY: 0.0000809 AC XY: 11AN XY: 135914
GnomAD4 exome AF: 0.0000410 AC: 60AN: 1461880Hom.: 0 Cov.: 32 AF XY: 0.0000495 AC XY: 36AN XY: 727246
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151994Hom.: 0 Cov.: 28 AF XY: 0.0000135 AC XY: 1AN XY: 74246
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 17, 2024 | The c.253G>A (p.A85T) alteration is located in exon 4 (coding exon 3) of the CLEC10A gene. This alteration results from a G to A substitution at nucleotide position 253, causing the alanine (A) at amino acid position 85 to be replaced by a threonine (T). 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