16-56343836-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_138736.3(GNAO1):c.951A>G(p.Lys317Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.371 in 1,580,160 control chromosomes in the GnomAD database, including 108,473 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_138736.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GNAO1 | NM_020988.3 | c.723+6976A>G | intron_variant | Intron 6 of 8 | ENST00000262493.12 | NP_066268.1 | ||
GNAO1 | NM_138736.3 | c.951A>G | p.Lys317Lys | synonymous_variant | Exon 8 of 8 | NP_620073.2 | ||
GNAO1 | XM_011523003.4 | c.597+6976A>G | intron_variant | Intron 6 of 8 | XP_011521305.1 | |||
GNAO1 | XR_007064866.1 | n.1698A>G | non_coding_transcript_exon_variant | Exon 8 of 9 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.465 AC: 55766AN: 119914Hom.: 9114 Cov.: 28
GnomAD3 exomes AF: 0.345 AC: 86379AN: 250710Hom.: 16095 AF XY: 0.348 AC XY: 47128AN XY: 135568
GnomAD4 exome AF: 0.363 AC: 530211AN: 1460142Hom.: 99337 Cov.: 34 AF XY: 0.364 AC XY: 264269AN XY: 726440
GnomAD4 genome AF: 0.465 AC: 55826AN: 120018Hom.: 9136 Cov.: 28 AF XY: 0.461 AC XY: 26876AN XY: 58342
ClinVar
Submissions by phenotype
not provided Benign:3
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not specified Benign:1
This variant is classified as Benign based on local population frequency. This variant was detected in 38% of patients studied in a panel designed for Epileptic and Developmental Encephalopathy and Progressive Myoclonus Epilepsy. Number of patients: 35. Only high quality variants are reported. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at