chr1-231241447-C-T
Position:
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_014236.4(GNPAT):c.69C>T(p.Leu23=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000411 in 1,459,590 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 (★).
Frequency
Genomes: not found (cov: 33)
Exomes 𝑓: 0.0000041 ( 0 hom. )
Consequence
GNPAT
NM_014236.4 synonymous
NM_014236.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.670
Genes affected
GNPAT (HGNC:4416): (glyceronephosphate O-acyltransferase) This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.77).
BP6
Variant 1-231241447-C-T is Benign according to our data. Variant chr1-231241447-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2805825.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.67 with no splicing effect.
Transcripts
RefSeq
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
|---|---|---|---|---|---|---|---|
| GNPAT | NM_014236.4 | c.69C>T | p.Leu23= | synonymous_variant | 1/16 | ENST00000366647.9 | |
| GNPAT | NM_001316350.2 | c.69C>T | p.Leu23= | synonymous_variant | 1/15 | ||
| GNPAT | XM_005273313.5 | c.69C>T | p.Leu23= | synonymous_variant | 1/16 |
Ensembl
| Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| GNPAT | ENST00000366647.9 | c.69C>T | p.Leu23= | synonymous_variant | 1/16 | 1 | NM_014236.4 | P1 | |
| GNPAT | ENST00000416000.1 | c.69C>T | p.Leu23= | synonymous_variant | 1/13 | 5 | |||
| GNPAT | ENST00000436239.5 | c.69C>T | p.Leu23= | synonymous_variant | 1/6 | 3 | |||
| GNPAT | ENST00000644483.1 | c.69C>T | p.Leu23= | synonymous_variant, NMD_transcript_variant | 1/17 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1459590Hom.: 0 Cov.: 31 AF XY: 0.00000138 AC XY: 1AN XY: 726300
GnomAD4 exome
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1459590
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31
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1
AN XY:
726300
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GnomAD4 genome
GnomAD4 genome
Cov.:
33
ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
| Likely benign, criteria provided, single submitter | clinical testing | Invitae | Sep 22, 2023 | - - |
Computational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at