6-41034951-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_173561.3(UNC5CL):c.124G>T(p.Ala42Ser) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000551 in 1,613,926 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_173561.3 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
UNC5CL | NM_173561.3 | c.124G>T | p.Ala42Ser | missense_variant | 2/9 | ENST00000244565.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
UNC5CL | ENST00000244565.8 | c.124G>T | p.Ala42Ser | missense_variant | 2/9 | 1 | NM_173561.3 | P1 | |
UNC5CL | ENST00000373164.1 | c.124G>T | p.Ala42Ser | missense_variant | 1/8 | 1 | P1 | ||
OARD1 | ENST00000482853.5 | c.*197G>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000460 AC: 7AN: 152146Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000955 AC: 24AN: 251380Hom.: 0 AF XY: 0.0000957 AC XY: 13AN XY: 135868
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461662Hom.: 0 Cov.: 31 AF XY: 0.0000619 AC XY: 45AN XY: 727084
GnomAD4 genome ? AF: 0.0000460 AC: 7AN: 152264Hom.: 0 Cov.: 33 AF XY: 0.0000672 AC XY: 5AN XY: 74450
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 22, 2023 | The c.124G>T (p.A42S) alteration is located in exon 2 (coding exon 1) of the UNC5CL gene. This alteration results from a G to T substitution at nucleotide position 124, causing the alanine (A) at amino acid position 42 to be replaced by a serine (S). 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