chr19-14151148-G-C
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 1P and 6B. PP2BP4_ModerateBS2
The NM_014921.5(ADGRL1):c.4135C>G(p.Leu1379Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000587 in 1,602,238 control chromosomes in the GnomAD database, including 1 homozygotes. 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. L1379R) has been classified as Uncertain significance.
Frequency
Consequence
NM_014921.5 missense
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 |
---|---|---|---|---|---|---|---|
ADGRL1 | NM_014921.5 | c.4135C>G | p.Leu1379Val | missense_variant | 23/23 | ENST00000361434.8 | |
ADGRL1-AS1 | NR_045214.1 | n.73-4004G>C | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRL1 | ENST00000361434.8 | c.4135C>G | p.Leu1379Val | missense_variant | 23/23 | 1 | NM_014921.5 | A1 | |
ADGRL1-AS1 | ENST00000588387.2 | n.79-4004G>C | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000723 AC: 11AN: 152092Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000769 AC: 17AN: 221184Hom.: 0 AF XY: 0.0000735 AC XY: 9AN XY: 122428
GnomAD4 exome AF: 0.0000572 AC: 83AN: 1450146Hom.: 1 Cov.: 37 AF XY: 0.0000624 AC XY: 45AN XY: 720804
GnomAD4 genome ? AF: 0.0000723 AC: 11AN: 152092Hom.: 0 Cov.: 32 AF XY: 0.0000673 AC XY: 5AN XY: 74294
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 27, 2022 | The c.4150C>G (p.L1384V) alteration is located in exon 24 (coding exon 23) of the ADGRL1 gene. This alteration results from a C to G substitution at nucleotide position 4150, causing the leucine (L) at amino acid position 1384 to be replaced by a valine (V). 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