chr8-37831499-G-A
Variant summary
Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2
The NM_032777.10(ADGRA2):c.1009G>A(p.Ala337Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000137 in 1,461,528 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_032777.10 missense
Scores
Clinical Significance
Conservation
Publications
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ACMG classification
Our verdict: Benign. The variant received -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
ADGRA2 | NM_032777.10 | c.1009G>A | p.Ala337Thr | missense_variant | Exon 8 of 19 | ENST00000412232.3 | NP_116166.9 | |
ADGRA2 | XM_011544481.3 | c.1009G>A | p.Ala337Thr | missense_variant | Exon 8 of 19 | XP_011542783.1 | ||
ADGRA2 | XM_011544482.3 | c.937G>A | p.Ala313Thr | missense_variant | Exon 7 of 18 | XP_011542784.1 | ||
ADGRA2 | XM_011544483.3 | c.1009G>A | p.Ala337Thr | missense_variant | Exon 8 of 18 | XP_011542785.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADGRA2 | ENST00000412232.3 | c.1009G>A | p.Ala337Thr | missense_variant | Exon 8 of 19 | 1 | NM_032777.10 | ENSP00000406367.2 | ||
ADGRA2 | ENST00000315215.11 | c.1009G>A | p.Ala337Thr | missense_variant | Exon 8 of 16 | 1 | ENSP00000323508.7 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD2 exomes AF: 0.00000798 AC: 2AN: 250740 AF XY: 0.0000147 show subpopulations
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461528Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727102 show subpopulations
Age Distribution
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1009G>A (p.A337T) alteration is located in exon 8 (coding exon 8) of the ADGRA2 gene. This alteration results from a G to A substitution at nucleotide position 1009, causing the alanine (A) at amino acid position 337 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