19-14151055-C-T
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBS1_SupportingBS2
The NM_014921.5(ADGRL1):c.4228G>A(p.Ala1410Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. 12/20 in silico tools predict 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. A1410V) has been classified as Uncertain significance.
Frequency
Consequence
NM_014921.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000589 AC: 7AN: 11882Hom.: 0 Cov.: 0
GnomAD3 exomes AF: 0.0000931 AC: 2AN: 21492Hom.: 0 AF XY: 0.000173 AC XY: 2AN XY: 11580
GnomAD4 exome AF: 0.0000340 AC: 8AN: 235254Hom.: 0 Cov.: 14 AF XY: 0.0000623 AC XY: 7AN XY: 112436
GnomAD4 genome AF: 0.000671 AC: 8AN: 11916Hom.: 0 Cov.: 0 AF XY: 0.000161 AC XY: 1AN XY: 6202
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.4243G>A (p.A1415T) alteration is located in exon 24 (coding exon 23) of the ADGRL1 gene. This alteration results from a G to A substitution at nucleotide position 4243, causing the alanine (A) at amino acid position 1415 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