rs140995132
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 0P and 2B. BP4_Moderate
The NM_006412.4(AGPAT2):c.208T>G(p.Phe70Val) variant causes a missense change. The variant allele was found at a frequency of 0.0000267 in 1,612,892 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 Uncertain significance (★★).
Frequency
Consequence
NM_006412.4 missense
Scores
Clinical Significance
Conservation
Publications
- congenital generalized lipodystrophy type 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), G2P
- Berardinelli-Seip congenital lipodystrophyInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
- neonatal diabetes mellitusInheritance: AR Classification: LIMITED Submitted by: Genomics England PanelApp
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_006412.4. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AGPAT2 | NM_006412.4 | MANE Select | c.208T>G | p.Phe70Val | missense | Exon 2 of 6 | NP_006403.2 | ||
| AGPAT2 | NM_001012727.2 | c.208T>G | p.Phe70Val | missense | Exon 2 of 5 | NP_001012745.1 |
Ensembl Transcripts
| Selected | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| AGPAT2 | ENST00000371696.7 | TSL:1 MANE Select | c.208T>G | p.Phe70Val | missense | Exon 2 of 6 | ENSP00000360761.2 | ||
| AGPAT2 | ENST00000371694.7 | TSL:1 | c.208T>G | p.Phe70Val | missense | Exon 2 of 5 | ENSP00000360759.3 | ||
| AGPAT2 | ENST00000470861.1 | TSL:2 | n.216T>G | non_coding_transcript_exon | Exon 2 of 2 |
Frequencies
GnomAD3 genomes AF: 0.000164 AC: 25AN: 152236Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.0000282 AC: 7AN: 248162 AF XY: 0.0000296 show subpopulations
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1460538Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 726590 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.000164 AC: 25AN: 152354Hom.: 0 Cov.: 33 AF XY: 0.000188 AC XY: 14AN XY: 74506 show subpopulations
Age Distribution
ClinVar
ClinVar submissions as Germline
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at