1-231241444-G-A
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014236.4(GNPAT):c.66G>A(p.Val22=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000342 in 1,459,936 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. V22V) has been classified as Likely benign.
Frequency
Consequence
NM_014236.4 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPAT | NM_014236.4 | c.66G>A | p.Val22= | synonymous_variant | 1/16 | ENST00000366647.9 | |
GNPAT | NM_001316350.2 | c.66G>A | p.Val22= | synonymous_variant | 1/15 | ||
GNPAT | XM_005273313.5 | c.66G>A | p.Val22= | synonymous_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPAT | ENST00000366647.9 | c.66G>A | p.Val22= | synonymous_variant | 1/16 | 1 | NM_014236.4 | P1 | |
GNPAT | ENST00000416000.1 | c.66G>A | p.Val22= | synonymous_variant | 1/13 | 5 | |||
GNPAT | ENST00000436239.5 | c.66G>A | p.Val22= | synonymous_variant | 1/6 | 3 | |||
GNPAT | ENST00000644483.1 | c.66G>A | p.Val22= | synonymous_variant, NMD_transcript_variant | 1/17 |
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD3 exomes AF: 0.00000402 AC: 1AN: 248970Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 134782
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1459936Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 726474
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 21, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at