8-6741710-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_018361.5(AGPAT5):c.545C>T(p.Thr182Ile) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000477 in 1,612,690 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_018361.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGPAT5 | NM_018361.5 | c.545C>T | p.Thr182Ile | missense_variant | 5/8 | ENST00000285518.11 | |
AGPAT5 | XM_047421938.1 | c.92C>T | p.Thr31Ile | missense_variant | 4/7 | ||
AGPAT5 | XM_047421939.1 | c.92C>T | p.Thr31Ile | missense_variant | 6/9 | ||
AGPAT5 | XM_047421940.1 | c.495+9060C>T | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGPAT5 | ENST00000285518.11 | c.545C>T | p.Thr182Ile | missense_variant | 5/8 | 1 | NM_018361.5 | P1 | |
AGPAT5 | ENST00000518327.1 | c.196-13341C>T | intron_variant | 1 | |||||
AGPAT5 | ENST00000530716.1 | n.225C>T | non_coding_transcript_exon_variant | 2/5 | 3 | ||||
AGPAT5 | ENST00000523234.5 | c.*208C>T | 3_prime_UTR_variant, NMD_transcript_variant | 4/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000283 AC: 43AN: 152144Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.0000959 AC: 24AN: 250206Hom.: 0 AF XY: 0.0000813 AC XY: 11AN XY: 135268
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1460428Hom.: 0 Cov.: 30 AF XY: 0.0000234 AC XY: 17AN XY: 726504
GnomAD4 genome ? AF: 0.000282 AC: 43AN: 152262Hom.: 0 Cov.: 33 AF XY: 0.000309 AC XY: 23AN XY: 74438
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 15, 2021 | The c.545C>T (p.T182I) alteration is located in exon 5 (coding exon 5) of the AGPAT5 gene. This alteration results from a C to T substitution at nucleotide position 545, causing the threonine (T) at amino acid position 182 to be replaced by an isoleucine (I). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at