chr2-151828148-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_012097.4(ARL5A):c.29G>A(p.Arg10Lys) variant causes a missense change. The variant allele was found at a frequency of 0.00000137 in 1,457,592 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_012097.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ARL5A | NM_012097.4 | c.29G>A | p.Arg10Lys | missense_variant | Exon 1 of 6 | ENST00000295087.13 | NP_036229.1 | |
ARL5A | NM_001037174.2 | c.-64+237G>A | intron_variant | Intron 1 of 5 | NP_001032251.1 | |||
ARL5A | NM_177985.3 | c.-66+241G>A | intron_variant | Intron 1 of 5 | NP_817114.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ARL5A | ENST00000295087.13 | c.29G>A | p.Arg10Lys | missense_variant | Exon 1 of 6 | 1 | NM_012097.4 | ENSP00000295087.8 | ||
ENSG00000283228 | ENST00000637559.1 | n.*333-12949G>A | intron_variant | Intron 10 of 11 | 5 | ENSP00000489697.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome AF: 0.00000137 AC: 2AN: 1457592Hom.: 0 Cov.: 30 AF XY: 0.00 AC XY: 0AN XY: 725098
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.29G>A (p.R10K) alteration is located in exon 1 (coding exon 1) of the ARL5A gene. This alteration results from a G to A substitution at nucleotide position 29, causing the arginine (R) at amino acid position 10 to be replaced by a lysine (K). 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