chr10-85723127-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The NM_017551.3(GRID1):c.1873G>A(p.Val625Met) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000255 in 1,607,446 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_017551.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRID1 | NM_017551.3 | c.1873G>A | p.Val625Met | missense_variant | 12/16 | ENST00000327946.12 | |
GRID1 | XM_047425122.1 | c.586G>A | p.Val196Met | missense_variant | 5/9 | ||
GRID1 | XM_047425123.1 | c.586G>A | p.Val196Met | missense_variant | 5/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRID1 | ENST00000327946.12 | c.1873G>A | p.Val625Met | missense_variant | 12/16 | 2 | NM_017551.3 | P1 | |
GRID1 | ENST00000464741.2 | c.1873G>A | p.Val625Met | missense_variant, NMD_transcript_variant | 12/15 | 1 |
Frequencies
GnomAD3 genomes AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000366 AC: 9AN: 246040Hom.: 0 AF XY: 0.0000301 AC XY: 4AN XY: 132902
GnomAD4 exome AF: 0.0000247 AC: 36AN: 1455252Hom.: 0 Cov.: 31 AF XY: 0.0000304 AC XY: 22AN XY: 723468
GnomAD4 genome AF: 0.0000329 AC: 5AN: 152194Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74342
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2021 | The c.1873G>A (p.V625M) alteration is located in exon 12 (coding exon 12) of the GRID1 gene. This alteration results from a G to A substitution at nucleotide position 1873, causing the valine (V) at amino acid position 625 to be replaced by a methionine (M). 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