11-36098356-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001304264.2(LDLRAD3):c.-131C>T variant causes a 5 prime UTR premature start codon gain change. The variant allele was found at a frequency of 0.0000489 in 1,614,052 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001304264.2 5_prime_UTR_premature_start_codon_gain
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
LDLRAD3 | NM_174902.4 | c.349C>T | p.Arg117Cys | missense_variant | Exon 4 of 6 | ENST00000315571.6 | NP_777562.1 | |
LDLRAD3 | NM_001304264.2 | c.-131C>T | 5_prime_UTR_premature_start_codon_gain_variant | Exon 3 of 6 | NP_001291193.1 | |||
LDLRAD3 | NM_001304263.2 | c.202C>T | p.Arg68Cys | missense_variant | Exon 3 of 5 | NP_001291192.1 | ||
LDLRAD3 | NM_001304264.2 | c.-131C>T | 5_prime_UTR_variant | Exon 3 of 6 | NP_001291193.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
LDLRAD3 | ENST00000315571.6 | c.349C>T | p.Arg117Cys | missense_variant | Exon 4 of 6 | 1 | NM_174902.4 | ENSP00000318607.5 | ||
LDLRAD3 | ENST00000528989.5 | c.202C>T | p.Arg68Cys | missense_variant | Exon 3 of 5 | 1 | ENSP00000433954.1 | |||
LDLRAD3 | ENST00000524419.5 | c.202C>T | p.Arg68Cys | missense_variant | Exon 3 of 6 | 5 | ENSP00000434313.1 | |||
LDLRAD3 | ENST00000532490.1 | n.303C>T | non_coding_transcript_exon_variant | Exon 4 of 5 | 4 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000148 AC: 37AN: 250506Hom.: 0 AF XY: 0.0000812 AC XY: 11AN XY: 135444
GnomAD4 exome AF: 0.0000534 AC: 78AN: 1461840Hom.: 0 Cov.: 31 AF XY: 0.0000454 AC XY: 33AN XY: 727222
GnomAD4 genome AF: 0.00000657 AC: 1AN: 152212Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74356
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.349C>T (p.R117C) alteration is located in exon 4 (coding exon 4) of the LDLRAD3 gene. This alteration results from a C to T substitution at nucleotide position 349, causing the arginine (R) at amino acid position 117 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