chr3-186853171-G-A
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2
The NM_004797.4(ADIPOQ):c.113G>A(p.Gly38Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000694 in 1,614,192 control chromosomes in the GnomAD database, including 7 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.0041 ( 4 hom., cov: 33)
Exomes 𝑓: 0.00034 ( 3 hom. )
Consequence
ADIPOQ
NM_004797.4 missense
NM_004797.4 missense
Scores
4
13
Clinical Significance
Conservation
PhyloP100: 2.54
Genes affected
ADIPOQ (HGNC:13633): (adiponectin, C1Q and collagen domain containing) This gene is expressed in adipose tissue exclusively. It encodes a protein with similarity to collagens X and VIII and complement factor C1q. The encoded protein circulates in the plasma and is involved with metabolic and hormonal processes. Mutations in this gene are associated with adiponectin deficiency. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Apr 2010]
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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 (MetaRNN=0.009943187).
BP6
?
Variant 3-186853171-G-A is Benign according to our data. Variant chr3-186853171-G-A is described in ClinVar as [Benign]. Clinvar id is 725273.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
?
High AC in GnomAd at 620 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ADIPOQ | NM_004797.4 | c.113G>A | p.Gly38Asp | missense_variant | 2/3 | ENST00000320741.7 | |
ADIPOQ-AS1 | NR_046662.2 | n.2287C>T | non_coding_transcript_exon_variant | 4/4 | |||
ADIPOQ | NM_001177800.2 | c.113G>A | p.Gly38Asp | missense_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ADIPOQ | ENST00000320741.7 | c.113G>A | p.Gly38Asp | missense_variant | 2/3 | 1 | NM_004797.4 | P1 | |
ADIPOQ | ENST00000444204.2 | c.113G>A | p.Gly38Asp | missense_variant | 3/4 | 1 | P1 | ||
ADIPOQ-AS1 | ENST00000422718.1 | n.2158C>T | non_coding_transcript_exon_variant | 3/3 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.00407 AC: 620AN: 152228Hom.: 4 Cov.: 33
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GnomAD3 exomes AF: 0.000972 AC: 244AN: 251128Hom.: 3 AF XY: 0.000700 AC XY: 95AN XY: 135746
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GnomAD4 exome AF: 0.000341 AC: 499AN: 1461844Hom.: 3 Cov.: 32 AF XY: 0.000311 AC XY: 226AN XY: 727226
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GnomAD4 genome ? AF: 0.00408 AC: 621AN: 152348Hom.: 4 Cov.: 33 AF XY: 0.00383 AC XY: 285AN XY: 74490
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 03, 2019 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
Cadd
Benign
Dann
Uncertain
DEOGEN2
Benign
T;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Uncertain
D
MetaRNN
Benign
T;T
MetaSVM
Uncertain
T
MutationAssessor
Benign
L;L
MutationTaster
Benign
N;N;N
PrimateAI
Benign
T
PROVEAN
Benign
N;N
REVEL
Uncertain
Sift
Benign
T;T
Sift4G
Benign
T;T
Polyphen
B;B
Vest4
MVP
ClinPred
T
GERP RS
Varity_R
gMVP
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at