13-100532344-C-A
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001195087.2(GGACT):c.248G>T(p.Ser83Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000113 in 1,550,506 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001195087.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GGACT | NM_001195087.2 | c.248G>T | p.Ser83Ile | missense_variant | Exon 3 of 3 | ENST00000683975.1 | NP_001182016.1 | |
GGACT | NM_033110.3 | c.248G>T | p.Ser83Ile | missense_variant | Exon 2 of 2 | NP_149101.1 | ||
GGACT | XM_011521129.4 | c.248G>T | p.Ser83Ile | missense_variant | Exon 3 of 3 | XP_011519431.1 | ||
GGACT | XM_047430708.1 | c.248G>T | p.Ser83Ile | missense_variant | Exon 3 of 3 | XP_047286664.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000125 AC: 19AN: 152220Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000220 AC: 33AN: 150232Hom.: 0 AF XY: 0.000187 AC XY: 15AN XY: 80304
GnomAD4 exome AF: 0.000112 AC: 156AN: 1398286Hom.: 0 Cov.: 31 AF XY: 0.000100 AC XY: 69AN XY: 689706
GnomAD4 genome AF: 0.000125 AC: 19AN: 152220Hom.: 0 Cov.: 33 AF XY: 0.000121 AC XY: 9AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.248G>T (p.S83I) alteration is located in exon 2 (coding exon 1) of the A2LD1 gene. This alteration results from a G to T substitution at nucleotide position 248, causing the serine (S) at amino acid position 83 to be replaced by an isoleucine (I). 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