chr22-32857293-T-C

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_000362.5(TIMP3):ā€‹c.249T>Cā€‹(p.His83=) variant causes a synonymous change. The variant allele was found at a frequency of 0.525 in 1,612,676 control chromosomes in the GnomAD database, including 228,674 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā˜…ā˜…).

Frequency

Genomes: š‘“ 0.61 ( 29994 hom., cov: 31)
Exomes š‘“: 0.52 ( 198680 hom. )

Consequence

TIMP3
NM_000362.5 synonymous

Scores

2

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:7

Conservation

PhyloP100: 4.55
Variant links:
Genes affected
TIMP3 (HGNC:11822): (TIMP metallopeptidase inhibitor 3) This gene belongs to the TIMP gene family. The proteins encoded by this gene family are inhibitors of the matrix metalloproteinases, a group of peptidases involved in degradation of the extracellular matrix (ECM). Expression of this gene is induced in response to mitogenic stimulation and this netrin domain-containing protein is localized to the ECM. Mutations in this gene have been associated with the autosomal dominant disorder Sorsby's fundus dystrophy. [provided by RefSeq, Jul 2008]
SYN3 (HGNC:11496): (synapsin III) This gene is a member of the synapsin gene family. Synapsins encode neuronal phosphoproteins which associate with the cytoplasmic surface of synaptic vesicles. Family members are characterized by common protein domains, and they are implicated in synaptogenesis and the modulation of neurotransmitter release, suggesting a potential role in several neuropsychiatric diseases. The protein encoded by this gene shares the synapsin family domain model, with domains A, C, and E exhibiting the highest degree of conservation. The protein contains a unique domain J, located between domains C and E. Based on this gene's localization to 22q12.3, a possible schizophrenia susceptibility locus, and the established neurobiological roles of the synapsins, this family member may represent a candidate gene for schizophrenia. The TIMP3 gene is located within an intron of this gene and is transcribed in the opposite direction. Alternative splicing of this gene results in multiple splice variants that encode different isoforms. [provided by RefSeq, Oct 2008]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.6).
BP6
Variant 22-32857293-T-C is Benign according to our data. Variant chr22-32857293-T-C is described in ClinVar as [Benign]. Clinvar id is 255943.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr22-32857293-T-C is described in Lovd as [Benign]. Variant chr22-32857293-T-C is described in Lovd as [Likely_benign].
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.828 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE Protein UniProt
TIMP3NM_000362.5 linkuse as main transcriptc.249T>C p.His83= synonymous_variant 3/5 ENST00000266085.7 NP_000353.1
SYN3NM_003490.4 linkuse as main transcriptc.711+7622A>G intron_variant ENST00000358763.7 NP_003481.3

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TIMP3ENST00000266085.7 linkuse as main transcriptc.249T>C p.His83= synonymous_variant 3/51 NM_000362.5 ENSP00000266085 P1
SYN3ENST00000358763.7 linkuse as main transcriptc.711+7622A>G intron_variant 5 NM_003490.4 ENSP00000351614 P1
SYN3ENST00000462268.1 linkuse as main transcriptn.225+7622A>G intron_variant, non_coding_transcript_variant 3

Frequencies

GnomAD3 genomes
AF:
0.609
AC:
92549
AN:
151848
Hom.:
29934
Cov.:
31
show subpopulations
Gnomad AFR
AF:
0.835
Gnomad AMI
AF:
0.715
Gnomad AMR
AF:
0.664
Gnomad ASJ
AF:
0.536
Gnomad EAS
AF:
0.609
Gnomad SAS
AF:
0.535
Gnomad FIN
AF:
0.438
Gnomad MID
AF:
0.576
Gnomad NFE
AF:
0.495
Gnomad OTH
AF:
0.594
GnomAD3 exomes
AF:
0.553
AC:
139046
AN:
251376
Hom.:
40026
AF XY:
0.541
AC XY:
73516
AN XY:
135852
show subpopulations
Gnomad AFR exome
AF:
0.834
Gnomad AMR exome
AF:
0.707
Gnomad ASJ exome
AF:
0.549
Gnomad EAS exome
AF:
0.583
Gnomad SAS exome
AF:
0.537
Gnomad FIN exome
AF:
0.429
Gnomad NFE exome
AF:
0.491
Gnomad OTH exome
AF:
0.535
GnomAD4 exome
AF:
0.516
AC:
753378
AN:
1460710
Hom.:
198680
Cov.:
49
AF XY:
0.514
AC XY:
373521
AN XY:
726704
show subpopulations
Gnomad4 AFR exome
AF:
0.845
Gnomad4 AMR exome
AF:
0.703
Gnomad4 ASJ exome
AF:
0.549
Gnomad4 EAS exome
AF:
0.643
Gnomad4 SAS exome
AF:
0.535
Gnomad4 FIN exome
AF:
0.429
Gnomad4 NFE exome
AF:
0.494
Gnomad4 OTH exome
AF:
0.538
GnomAD4 genome
AF:
0.610
AC:
92670
AN:
151966
Hom.:
29994
Cov.:
31
AF XY:
0.607
AC XY:
45041
AN XY:
74258
show subpopulations
Gnomad4 AFR
AF:
0.835
Gnomad4 AMR
AF:
0.665
Gnomad4 ASJ
AF:
0.536
Gnomad4 EAS
AF:
0.609
Gnomad4 SAS
AF:
0.534
Gnomad4 FIN
AF:
0.438
Gnomad4 NFE
AF:
0.495
Gnomad4 OTH
AF:
0.591
Alfa
AF:
0.525
Hom.:
35200
Bravo
AF:
0.638
Asia WGS
AF:
0.621
AC:
2157
AN:
3478
EpiCase
AF:
0.498
EpiControl
AF:
0.503

ClinVar

Significance: Benign
Submissions summary: Benign:7
Revision: criteria provided, multiple submitters, no conflicts
LINK: link

Submissions by phenotype

not provided Benign:3
Benign, criteria provided, single submitterclinical testingGeneDxMar 03, 2015- -
Benign, criteria provided, single submitterclinical testingLabcorp Genetics (formerly Invitae), LabcorpJan 31, 2024- -
Benign, criteria provided, single submitternot providedBreakthrough Genomics, Breakthrough Genomics-- -
Sorsby fundus dystrophy Benign:2
Benign, criteria provided, single submitterclinical testingGenome-Nilou LabSep 10, 2021- -
Benign, criteria provided, single submitterclinical testingIllumina Laboratory Services, IlluminaJan 13, 2018This 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. -
not specified Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact Sciences-- -
Fundus dystrophy, pseudoinflammatory, recessive form Benign:1
Benign, criteria provided, single submitterclinical testingMendelicsMay 28, 2019- -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.60
CADD
Benign
12
DANN
Benign
0.89
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.7

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: rs9862; hg19: chr22-33253280; COSMIC: COSV56662105; API