8-37831448-G-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_032777.10(ADGRA2):c.958G>T(p.Val320Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000453 in 1,612,402 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/22 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 Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADGRA2 | NM_032777.10 | c.958G>T | p.Val320Leu | missense_variant | 8/19 | ENST00000412232.3 | |
ADGRA2 | XM_011544481.3 | c.958G>T | p.Val320Leu | missense_variant | 8/19 | ||
ADGRA2 | XM_011544482.3 | c.886G>T | p.Val296Leu | missense_variant | 7/18 | ||
ADGRA2 | XM_011544483.3 | c.958G>T | p.Val320Leu | missense_variant | 8/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADGRA2 | ENST00000412232.3 | c.958G>T | p.Val320Leu | missense_variant | 8/19 | 1 | NM_032777.10 | P1 | |
ADGRA2 | ENST00000315215.11 | c.958G>T | p.Val320Leu | missense_variant | 8/16 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000328 AC: 5AN: 152238Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000683 AC: 17AN: 248938Hom.: 0 AF XY: 0.0000741 AC XY: 10AN XY: 134910
GnomAD4 exome AF: 0.0000466 AC: 68AN: 1460164Hom.: 0 Cov.: 32 AF XY: 0.0000468 AC XY: 34AN XY: 726540
GnomAD4 genome ? AF: 0.0000328 AC: 5AN: 152238Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74378
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 29, 2021 | The c.958G>T (p.V320L) alteration is located in exon 8 (coding exon 8) of the ADGRA2 gene. This alteration results from a G to T substitution at nucleotide position 958, causing the valine (V) at amino acid position 320 to be replaced by a leucine (L). 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