rs375808894
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Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_006412.4(AGPAT2):c.*10C>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 0.0000611 in 1,572,122 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00018 ( 0 hom., cov: 34)
Exomes 𝑓: 0.000049 ( 2 hom. )
Consequence
AGPAT2
NM_006412.4 3_prime_UTR
NM_006412.4 3_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.248
Genes affected
AGPAT2 (HGNC:325): (1-acylglycerol-3-phosphate O-acyltransferase 2) This gene encodes a member of the 1-acylglycerol-3-phosphate O-acyltransferase family. The protein is located within the endoplasmic reticulum membrane and converts lysophosphatidic acid to phosphatidic acid, the second step in de novo phospholipid biosynthesis. Mutations in this gene have been associated with congenital generalized lipodystrophy (CGL), or Berardinelli-Seip syndrome, a disease characterized by a near absence of adipose tissue and severe insulin resistance. Alternate transcriptional splice variants, encoding different isoforms, have been characterized. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -10 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.83).
BP6
?
Variant 9-136673742-G-A is Benign according to our data. Variant chr9-136673742-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 259975.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High Homozygotes in GnomAdExome4 at 2 AR gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
AGPAT2 | NM_006412.4 | c.*10C>T | 3_prime_UTR_variant | 6/6 | ENST00000371696.7 | ||
AGPAT2 | NM_001012727.2 | c.*10C>T | 3_prime_UTR_variant | 5/5 | |||
AGPAT2 | XM_047422636.1 | c.*10C>T | 3_prime_UTR_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
AGPAT2 | ENST00000371696.7 | c.*10C>T | 3_prime_UTR_variant | 6/6 | 1 | NM_006412.4 | P1 | ||
AGPAT2 | ENST00000371694.7 | c.*10C>T | 3_prime_UTR_variant | 5/5 | 1 | ||||
AGPAT2 | ENST00000472820.1 | n.775C>T | non_coding_transcript_exon_variant | 4/4 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.000177 AC: 27AN: 152220Hom.: 0 Cov.: 34
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GnomAD3 exomes AF: 0.0000701 AC: 14AN: 199752Hom.: 1 AF XY: 0.000102 AC XY: 11AN XY: 107918
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GnomAD4 exome AF: 0.0000486 AC: 69AN: 1419784Hom.: 2 Cov.: 31 AF XY: 0.0000484 AC XY: 34AN XY: 702046
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GnomAD4 genome ? AF: 0.000177 AC: 27AN: 152338Hom.: 0 Cov.: 34 AF XY: 0.000188 AC XY: 14AN XY: 74502
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at