chr1-231241332-C-T
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Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_014236.4(GNPAT):c.-47C>T variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000526 in 1,521,032 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 not provided (no stars).
Frequency
Genomes: 𝑓 0.0000066 ( 0 hom., cov: 33)
Exomes 𝑓: 0.0000051 ( 0 hom. )
Consequence
GNPAT
NM_014236.4 5_prime_UTR
NM_014236.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.375
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 -2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GNPAT | NM_014236.4 | c.-47C>T | 5_prime_UTR_variant | 1/16 | ENST00000366647.9 | ||
GNPAT | NM_001316350.2 | c.-47C>T | 5_prime_UTR_variant | 1/15 | |||
GNPAT | XM_005273313.5 | c.-47C>T | 5_prime_UTR_variant | 1/16 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GNPAT | ENST00000366647.9 | c.-47C>T | 5_prime_UTR_variant | 1/16 | 1 | NM_014236.4 | P1 | ||
GNPAT | ENST00000416000.1 | c.-47C>T | 5_prime_UTR_variant | 1/13 | 5 | ||||
GNPAT | ENST00000436239.5 | c.-47C>T | 5_prime_UTR_variant | 1/6 | 3 | ||||
GNPAT | ENST00000644483.1 | c.-47C>T | 5_prime_UTR_variant, NMD_transcript_variant | 1/17 |
Frequencies
GnomAD3 genomes AF: 0.00000657 AC: 1AN: 152234Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249778Hom.: 0 AF XY: 0.00000740 AC XY: 1AN XY: 135132
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GnomAD4 exome AF: 0.00000511 AC: 7AN: 1368680Hom.: 0 Cov.: 21 AF XY: 0.00000728 AC XY: 5AN XY: 686582
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GnomAD4 genome AF: 0.00000656 AC: 1AN: 152352Hom.: 0 Cov.: 33 AF XY: 0.0000134 AC XY: 1AN XY: 74494
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ClinVar
Significance: not provided
Submissions summary: Other:1
Revision: no classification provided
LINK: link
Submissions by phenotype
not provided Other:1
not provided, no classification provided | in vitro | Seelig Lab, University of Washington | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at