chr13-52703656-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_007015.3(CNMD):c.944C>T(p.Ser315Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00034 in 1,613,986 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/20 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.944C>T | p.Ser315Leu | missense_variant | 7/7 | ENST00000377962.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CNMD | ENST00000377962.8 | c.944C>T | p.Ser315Leu | missense_variant | 7/7 | 1 | NM_007015.3 | P4 | |
CNMD | ENST00000448904.6 | c.941C>T | p.Ser314Leu | missense_variant | 7/7 | 1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.000276 AC: 42AN: 152198Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000219 AC: 55AN: 251134Hom.: 0 AF XY: 0.000221 AC XY: 30AN XY: 135720
GnomAD4 exome AF: 0.000346 AC: 506AN: 1461788Hom.: 0 Cov.: 31 AF XY: 0.000330 AC XY: 240AN XY: 727190
GnomAD4 genome ? AF: 0.000276 AC: 42AN: 152198Hom.: 0 Cov.: 33 AF XY: 0.000296 AC XY: 22AN XY: 74346
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 01, 2022 | The c.944C>T (p.S315L) alteration is located in exon 7 (coding exon 7) of the LECT1 gene. This alteration results from a C to T substitution at nucleotide position 944, causing the serine (S) at amino acid position 315 to be replaced by a leucine (L). 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