chr8-6730740-A-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_018361.5(AGPAT5):c.319A>G(p.Ile107Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000428 in 1,613,306 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 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 Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGPAT5 | NM_018361.5 | c.319A>G | p.Ile107Val | missense_variant | 3/8 | ENST00000285518.11 | |
AGPAT5 | XM_047421940.1 | c.319A>G | p.Ile107Val | missense_variant | 3/5 | ||
AGPAT5 | XM_047421938.1 | c.-135A>G | 5_prime_UTR_variant | 2/7 | |||
AGPAT5 | XM_047421939.1 | c.-135A>G | 5_prime_UTR_variant | 4/9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGPAT5 | ENST00000285518.11 | c.319A>G | p.Ile107Val | missense_variant | 3/8 | 1 | NM_018361.5 | P1 | |
AGPAT5 | ENST00000518327.1 | c.195+21853A>G | intron_variant | 1 | |||||
AGPAT5 | ENST00000523234.5 | c.249A>G | p.Pro83= | synonymous_variant, NMD_transcript_variant | 2/7 | 5 | |||
AGPAT5 | ENST00000523586.1 | c.*251A>G | 3_prime_UTR_variant, NMD_transcript_variant | 4/4 | 4 |
Frequencies
GnomAD3 genomes ? AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251406Hom.: 0 AF XY: 0.00000736 AC XY: 1AN XY: 135888
GnomAD4 exome AF: 0.0000411 AC: 60AN: 1461116Hom.: 0 Cov.: 31 AF XY: 0.0000440 AC XY: 32AN XY: 726844
GnomAD4 genome ? AF: 0.0000591 AC: 9AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.0000538 AC XY: 4AN XY: 74324
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 08, 2022 | The c.319A>G (p.I107V) alteration is located in exon 3 (coding exon 3) of the AGPAT5 gene. This alteration results from a A to G substitution at nucleotide position 319, causing the isoleucine (I) at amino acid position 107 to be replaced by a valine (V). 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