4-61892712-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001387552.1(ADGRL3):c.1537C>T(p.Arg513Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000192 in 1,613,822 control chromosomes in the GnomAD database, with no homozygous occurrence. 12/18 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001387552.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADGRL3 | NM_001387552.1 | c.1537C>T | p.Arg513Trp | missense_variant | Exon 10 of 27 | ENST00000683033.1 | NP_001374481.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRL3 | ENST00000683033.1 | c.1537C>T | p.Arg513Trp | missense_variant | Exon 10 of 27 | NM_001387552.1 | ENSP00000507980.1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000441 AC: 11AN: 249200Hom.: 0 AF XY: 0.0000592 AC XY: 8AN XY: 135200
GnomAD4 exome AF: 0.0000185 AC: 27AN: 1461688Hom.: 0 Cov.: 31 AF XY: 0.0000234 AC XY: 17AN XY: 727128
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152134Hom.: 0 Cov.: 31 AF XY: 0.0000135 AC XY: 1AN XY: 74332
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1333C>T (p.R445W) alteration is located in exon 7 (coding exon 7) of the ADGRL3 gene. This alteration results from a C to T substitution at nucleotide position 1333, causing the arginine (R) at amino acid position 445 to be replaced by a tryptophan (W). 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