chr8-6708851-G-T
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Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_018361.5(AGPAT5):c.183G>T(p.Met61Ile) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000048 in 1,457,600 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000048 ( 0 hom. )
Consequence
AGPAT5
NM_018361.5 missense
NM_018361.5 missense
Scores
2
8
8
Clinical Significance
Conservation
PhyloP100: 7.30
Genes affected
AGPAT5 (HGNC:20886): (1-acylglycerol-3-phosphate O-acyltransferase 5) This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. This integral membrane protein converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. A pseudogene of this gene is present on the Y chromosome. [provided by RefSeq, Aug 2014]
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ACMG classification
Classification made for transcript
Verdict is Uncertain_significance. Variant got 2 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGPAT5 | NM_018361.5 | c.183G>T | p.Met61Ile | missense_variant | 1/8 | ENST00000285518.11 | |
AGPAT5 | XM_047421940.1 | c.183G>T | p.Met61Ile | missense_variant | 1/5 | ||
AGPAT5 | XM_047421938.1 | c.-201G>T | 5_prime_UTR_variant | 1/7 | |||
AGPAT5 | XM_047421939.1 | c.-333G>T | 5_prime_UTR_variant | 1/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGPAT5 | ENST00000285518.11 | c.183G>T | p.Met61Ile | missense_variant | 1/8 | 1 | NM_018361.5 | P1 | |
AGPAT5 | ENST00000518327.1 | c.160G>T | p.Gly54Cys | missense_variant | 1/3 | 1 | |||
AGPAT5 | ENST00000523234.5 | c.183G>T | p.Met61Ile | missense_variant, NMD_transcript_variant | 1/7 | 5 | |||
AGPAT5 | ENST00000523586.1 | upstream_gene_variant | 4 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD3 genomes
Cov.:
32
GnomAD3 exomes AF: 0.00000816 AC: 2AN: 245166Hom.: 0 AF XY: 0.00000750 AC XY: 1AN XY: 133300
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GnomAD4 exome AF: 0.00000480 AC: 7AN: 1457600Hom.: 0 Cov.: 31 AF XY: 0.00000552 AC XY: 4AN XY: 725028
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GnomAD4 genome Cov.: 32
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32
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ClinVar
Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 09, 2024 | The c.183G>T (p.M61I) alteration is located in exon 1 (coding exon 1) of the AGPAT5 gene. This alteration results from a G to T substitution at nucleotide position 183, causing the methionine (M) at amino acid position 61 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Uncertain
D
BayesDel_noAF
Uncertain
CADD
Uncertain
DANN
Benign
DEOGEN2
Benign
T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
M_CAP
Pathogenic
D
MetaRNN
Uncertain
D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M
MutationTaster
Benign
D
PrimateAI
Uncertain
T
PROVEAN
Benign
N
REVEL
Uncertain
Sift
Benign
T
Sift4G
Benign
T
Polyphen
B
Vest4
MutPred
Loss of catalytic residue at V57 (P = 0.0601);
MVP
MPC
ClinPred
D
GERP RS
Varity_R
gMVP
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