chr6-41032063-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4
The NM_173561.3(UNC5CL):c.1024C>T(p.Arg342Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00083 in 1,614,176 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. R342L) has been classified as Uncertain significance.
Frequency
Consequence
NM_173561.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC5CL | NM_173561.3 | c.1024C>T | p.Arg342Cys | missense_variant | 5/9 | ENST00000244565.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC5CL | ENST00000244565.8 | c.1024C>T | p.Arg342Cys | missense_variant | 5/9 | 1 | NM_173561.3 | P1 | |
UNC5CL | ENST00000373164.1 | c.1024C>T | p.Arg342Cys | missense_variant | 4/8 | 1 | P1 | ||
UNC5CL | ENST00000470102.1 | n.179C>T | non_coding_transcript_exon_variant | 2/5 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000466 AC: 71AN: 152200Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000489 AC: 123AN: 251396Hom.: 0 AF XY: 0.000500 AC XY: 68AN XY: 135876
GnomAD4 exome AF: 0.000868 AC: 1269AN: 1461858Hom.: 0 Cov.: 31 AF XY: 0.000842 AC XY: 612AN XY: 727232
GnomAD4 genome ? AF: 0.000466 AC: 71AN: 152318Hom.: 0 Cov.: 33 AF XY: 0.000470 AC XY: 35AN XY: 74494
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 24, 2022 | The c.1024C>T (p.R342C) alteration is located in exon 5 (coding exon 4) of the UNC5CL gene. This alteration results from a C to T substitution at nucleotide position 1024, causing the arginine (R) at amino acid position 342 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