chr13-52724005-A-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007015.3(CNMD):c.460T>A(p.Ser154Thr) variant causes a missense change. The variant allele was found at a frequency of 0.000000687 in 1,456,238 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_007015.3 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 |
---|---|---|---|---|---|---|---|
CNMD | NM_007015.3 | c.460T>A | p.Ser154Thr | missense_variant | 4/7 | ENST00000377962.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNMD | ENST00000377962.8 | c.460T>A | p.Ser154Thr | missense_variant | 4/7 | 1 | NM_007015.3 | P4 | |
CNMD | ENST00000448904.6 | c.460T>A | p.Ser154Thr | missense_variant | 4/7 | 1 | A1 | ||
CNMD | ENST00000431550.1 | c.226T>A | p.Ser76Thr | missense_variant | 3/4 | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome AF: 6.87e-7 AC: 1AN: 1456238Hom.: 0 Cov.: 29 AF XY: 0.00000138 AC XY: 1AN XY: 724852
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 12, 2021 | The c.460T>A (p.S154T) alteration is located in exon 4 (coding exon 4) of the LECT1 gene. This alteration results from a T to A substitution at nucleotide position 460, causing the serine (S) at amino acid position 154 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
Publications
No publications associated with this variant yet.