chr19-14587621-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001204118.2(CLEC17A):c.129G>T(p.Met43Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another nucleotide change resulting in same amino acid change has been previously reported as Uncertain significancein ClinVar.
Frequency
Consequence
NM_001204118.2 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 | UniProt |
---|---|---|---|---|---|---|---|
CLEC17A | NM_001204118.2 | c.129G>T | p.Met43Ile | missense_variant | 3/14 | ENST00000417570.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CLEC17A | ENST00000417570.6 | c.129G>T | p.Met43Ile | missense_variant | 3/14 | 1 | NM_001204118.2 | P1 | |
CLEC17A | ENST00000339847.9 | c.129G>T | p.Met43Ile | missense_variant, NMD_transcript_variant | 3/13 | 1 | |||
CLEC17A | ENST00000551730.1 | c.129G>T | p.Met43Ile | missense_variant, NMD_transcript_variant | 3/14 | 1 | |||
CLEC17A | ENST00000547437.5 | c.129G>T | p.Met43Ile | missense_variant | 3/13 | 2 |
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD3 exomes AF: 0.00000564 AC: 1AN: 177376Hom.: 0 AF XY: 0.0000106 AC XY: 1AN XY: 94734
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000212 AC: 3AN: 1417306Hom.: 0 Cov.: 32 AF XY: 0.00000142 AC XY: 1AN XY: 703124
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.129G>T (p.M43I) alteration is located in exon 3 (coding exon 3) of the CLEC17A gene. This alteration results from a G to T substitution at nucleotide position 129, causing the methionine (M) at amino acid position 43 to be replaced by an isoleucine (I). 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