chr8-37831499-G-A
Variant summary
Our verdict is Benign. Variant got -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. 15/20 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
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ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRA2 | NM_032777.10 | c.1009G>A | p.Ala337Thr | missense_variant | 8/19 | ENST00000412232.3 | |
ADGRA2 | XM_011544481.3 | c.1009G>A | p.Ala337Thr | missense_variant | 8/19 | ||
ADGRA2 | XM_011544482.3 | c.937G>A | p.Ala313Thr | missense_variant | 7/18 | ||
ADGRA2 | XM_011544483.3 | c.1009G>A | p.Ala337Thr | missense_variant | 8/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRA2 | ENST00000412232.3 | c.1009G>A | p.Ala337Thr | missense_variant | 8/19 | 1 | NM_032777.10 | P1 | |
ADGRA2 | ENST00000315215.11 | c.1009G>A | p.Ala337Thr | missense_variant | 8/16 | 1 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000798 AC: 2AN: 250740Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135688
GnomAD4 exome AF: 0.0000137 AC: 20AN: 1461528Hom.: 0 Cov.: 32 AF XY: 0.0000138 AC XY: 10AN XY: 727102
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jun 06, 2022 | 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