16-30748488-C-G
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_000294.3(PHKG2):c.-21C>G variant causes a splice region, 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000597 in 401,956 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 3/3 splice prediction tools predict no significant impact on normal splicing. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_000294.3 splice_region, 5_prime_UTR
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 | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PHKG2 | NM_000294.3 | c.-21C>G | splice_region_variant, 5_prime_UTR_variant | 1/10 | ENST00000563588.6 | NP_000285.1 | ||
PHKG2 | NM_001172432.2 | c.-21C>G | splice_region_variant, 5_prime_UTR_variant | 1/11 | NP_001165903.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
PHKG2 | ENST00000563588.6 | c.-21C>G | splice_region_variant, 5_prime_UTR_variant | 1/10 | 1 | NM_000294.3 | ENSP00000455607 | P4 |
Frequencies
GnomAD3 genomes AF: 0.000131 AC: 20AN: 152268Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.0000160 AC: 4AN: 249570Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 130424
GnomAD4 genome AF: 0.000131 AC: 20AN: 152386Hom.: 0 Cov.: 34 AF XY: 0.000107 AC XY: 8AN XY: 74516
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 07, 2016 | This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at