chr9-136673595-G-A
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1
The NM_006412.4(AGPAT2):c.*157C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.826 in 827,698 control chromosomes in the GnomAD database, including 284,370 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_006412.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
AGPAT2 | NM_006412.4 | c.*157C>T | 3_prime_UTR_variant | Exon 6 of 6 | ENST00000371696.7 | NP_006403.2 | ||
AGPAT2 | NM_001012727.2 | c.*157C>T | 3_prime_UTR_variant | Exon 5 of 5 | NP_001012745.1 | |||
AGPAT2 | XM_047422636.1 | c.*157C>T | 3_prime_UTR_variant | Exon 6 of 6 | XP_047278592.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
AGPAT2 | ENST00000371696 | c.*157C>T | 3_prime_UTR_variant | Exon 6 of 6 | 1 | NM_006412.4 | ENSP00000360761.2 | |||
AGPAT2 | ENST00000371694 | c.*157C>T | 3_prime_UTR_variant | Exon 5 of 5 | 1 | ENSP00000360759.3 | ||||
AGPAT2 | ENST00000472820.1 | n.*114C>T | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.777 AC: 118144AN: 152010Hom.: 46770 Cov.: 34
GnomAD4 exome AF: 0.837 AC: 565654AN: 675570Hom.: 237607 Cov.: 9 AF XY: 0.839 AC XY: 283784AN XY: 338252
GnomAD4 genome AF: 0.777 AC: 118165AN: 152128Hom.: 46763 Cov.: 34 AF XY: 0.780 AC XY: 58030AN XY: 74376
ClinVar
Submissions by phenotype
not provided Benign:2
- -
- -
Congenital generalized lipodystrophy type 1 Benign:2
- -
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at