chr7-2814361-C-T
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_001282441.2(GNA12):c.83G>A(p.Arg28Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00774 in 1,603,128 control chromosomes in the GnomAD database, including 76 homozygotes. In-silico tool predicts a benign outcome for this variant. 11/13 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_001282441.2 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNA12 | NM_007353.3 | c.310-19218G>A | intron_variant | Intron 1 of 3 | ENST00000275364.8 | NP_031379.2 | ||
GNA12 | NM_001282441.2 | c.83G>A | p.Arg28Gln | missense_variant | Exon 2 of 5 | NP_001269370.1 | ||
GNA12 | NM_001293092.2 | c.310-19218G>A | intron_variant | Intron 1 of 2 | NP_001280021.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GNA12 | ENST00000275364.8 | c.310-19218G>A | intron_variant | Intron 1 of 3 | 1 | NM_007353.3 | ENSP00000275364.3 | |||
GNA12 | ENST00000407904.7 | c.83G>A | p.Arg28Gln | missense_variant | Exon 2 of 5 | 2 | ENSP00000385935.3 | |||
GNA12 | ENST00000447791.1 | c.54+516G>A | intron_variant | Intron 1 of 1 | 4 | ENSP00000391462.1 |
Frequencies
GnomAD3 genomes AF: 0.00594 AC: 902AN: 151892Hom.: 6 Cov.: 31
GnomAD3 exomes AF: 0.00607 AC: 1467AN: 241542Hom.: 11 AF XY: 0.00655 AC XY: 869AN XY: 132636
GnomAD4 exome AF: 0.00793 AC: 11507AN: 1451118Hom.: 70 Cov.: 27 AF XY: 0.00785 AC XY: 5671AN XY: 722500
GnomAD4 genome AF: 0.00595 AC: 904AN: 152010Hom.: 6 Cov.: 31 AF XY: 0.00583 AC XY: 433AN XY: 74288
ClinVar
Submissions by phenotype
not provided Benign:1
GNA12: BP4, BS2 -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at