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GeneBe

3-186854218-C-T

Variant summary

Our verdict is Benign. Variant got -11 ACMG points: 0P and 11B. BP4_StrongBP6_ModerateBP7BS2

The NM_004797.4(ADIPOQ):c.249C>T(p.Thr83=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000313 in 1,613,376 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).

Frequency

Genomes: 𝑓 0.00051 ( 0 hom., cov: 31)
Exomes 𝑓: 0.00029 ( 1 hom. )

Consequence

ADIPOQ
NM_004797.4 synonymous

Scores

2

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -1.24
Variant links:
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]
ADIPOQ-AS1 (HGNC:40648): (ADIPOQ antisense RNA 1)

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -11 ACMG points.

BP4
?
    BP4 - Multiple lines of computational evidence suggest no impact on gene or gene product (conservation, evolutionary, splicing impact, etc.)
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-186854218-C-T is Benign according to our data. Variant chr3-186854218-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 730481.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
    BP7 - A synonymous (silent) variant for which splicing prediction algorithms predict no impact to the splice consensus sequence nor the creation of a new splice site AND the nucleotide is not highly conserved
Synonymous conserved (PhyloP=-1.24 with no splicing effect.
BS2
?
    BS2 - Observed in a healthy adult individual for a recessive (homozygous), dominant (heterozygous), or X-linked (hemizygous) disorder, with full penetrance expected at an early age
High AC in GnomAd at 77 AD gene.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
ADIPOQNM_004797.4 linkuse as main transcriptc.249C>T p.Thr83= synonymous_variant 3/3 ENST00000320741.7
ADIPOQ-AS1NR_046662.2 linkuse as main transcriptn.2035G>A non_coding_transcript_exon_variant 2/4
ADIPOQNM_001177800.2 linkuse as main transcriptc.249C>T p.Thr83= synonymous_variant 4/4

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
ADIPOQENST00000320741.7 linkuse as main transcriptc.249C>T p.Thr83= synonymous_variant 3/31 NM_004797.4 P1
ADIPOQENST00000444204.2 linkuse as main transcriptc.249C>T p.Thr83= synonymous_variant 4/41 P1
ADIPOQ-AS1ENST00000422718.1 linkuse as main transcriptn.1906G>A non_coding_transcript_exon_variant 1/35

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000506
AC:
77
AN:
152190
Hom.:
0
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00658
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.000283
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000867
Gnomad OTH
AF:
0.000956
GnomAD3 exomes
AF:
0.000275
AC:
69
AN:
250904
Hom.:
0
AF XY:
0.000273
AC XY:
37
AN XY:
135606
show subpopulations
Gnomad AFR exome
AF:
0.000123
Gnomad AMR exome
AF:
0.0000290
Gnomad ASJ exome
AF:
0.0000999
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.0000328
Gnomad FIN exome
AF:
0.000278
Gnomad NFE exome
AF:
0.000484
Gnomad OTH exome
AF:
0.000491
GnomAD4 exome
AF:
0.000293
AC:
428
AN:
1461068
Hom.:
1
Cov.:
31
AF XY:
0.000312
AC XY:
227
AN XY:
726754
show subpopulations
Gnomad4 AFR exome
AF:
0.0000299
Gnomad4 AMR exome
AF:
0.0000448
Gnomad4 ASJ exome
AF:
0.0000767
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000696
Gnomad4 FIN exome
AF:
0.000356
Gnomad4 NFE exome
AF:
0.000345
Gnomad4 OTH exome
AF:
0.000232
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.000506
AC:
77
AN:
152308
Hom.:
0
Cov.:
31
AF XY:
0.000564
AC XY:
42
AN XY:
74480
show subpopulations
Gnomad4 AFR
AF:
0.000168
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.000283
Gnomad4 NFE
AF:
0.000867
Gnomad4 OTH
AF:
0.000946
Alfa
AF:
0.000503
Hom.:
0
Bravo
AF:
0.000344
Asia WGS
AF:
0.000577
AC:
2
AN:
3478
EpiCase
AF:
0.000763
EpiControl
AF:
0.000119

ClinVar

Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not provided Benign:1
Likely benign, criteria provided, single submitterclinical testingInvitaeJan 04, 2018- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.75
Cadd
Benign
3.8
Dann
Benign
0.80

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs76533408; hg19: chr3-186572007; COSMIC: COSV57860060; API