chr4-61892956-T-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_001387552.1(ADGRL3):āc.1781T>Cā(p.Ile594Thr) variant causes a missense, splice region change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000727 in 1,513,756 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. I594V) has been classified as Uncertain significance.
Frequency
Consequence
NM_001387552.1 missense, splice_region
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRL3 | NM_001387552.1 | c.1781T>C | p.Ile594Thr | missense_variant, splice_region_variant | 10/27 | ENST00000683033.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRL3 | ENST00000683033.1 | c.1781T>C | p.Ile594Thr | missense_variant, splice_region_variant | 10/27 | NM_001387552.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000259 AC: 4AN: 154480Hom.: 0 AF XY: 0.0000123 AC XY: 1AN XY: 81074
GnomAD4 exome AF: 0.00000661 AC: 9AN: 1361568Hom.: 0 Cov.: 31 AF XY: 0.00000599 AC XY: 4AN XY: 667712
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152188Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74338
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 05, 2021 | The c.1577T>C (p.I526T) alteration is located in exon 7 (coding exon 7) of the ADGRL3 gene. This alteration results from a T to C substitution at nucleotide position 1577, causing the isoleucine (I) at amino acid position 526 to be replaced by a threonine (T). 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