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GeneBe

3-172329071-T-C

Variant summary

Our verdict is Benign. Variant got -15 ACMG points: 0P and 15B. BP4_StrongBP6_ModerateBP7BA1

The NM_022763.4(FNDC3B):c.1374T>C(p.Gly458=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.446 in 1,611,500 control chromosomes in the GnomAD database, including 165,850 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.51 ( 21035 hom., cov: 32)
Exomes 𝑓: 0.44 ( 144815 hom. )

Consequence

FNDC3B
NM_022763.4 synonymous

Scores

2

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.891
Variant links:
Genes affected
FNDC3B (HGNC:24670): (fibronectin type III domain containing 3B) Enables RNA binding activity. Predicted to act upstream of or within several processes, including negative regulation of osteoblast differentiation; substrate adhesion-dependent cell spreading; and type II pneumocyte differentiation. Predicted to be located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -15 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=-0.64).
BP6
?
    BP6 - Reputable source recently reports variant as benign, but the evidence is not available to the laboratory to perform an independent evaluation
Variant 3-172329071-T-C is Benign according to our data. Variant chr3-172329071-T-C is described in ClinVar as [Benign]. Clinvar id is 3059521.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=0.891 with no splicing effect.
BA1
?
    BA1 - Allele frequency is >5% in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.669 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
FNDC3BNM_022763.4 linkuse as main transcriptc.1374T>C p.Gly458= synonymous_variant 12/26 ENST00000415807.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
FNDC3BENST00000415807.7 linkuse as main transcriptc.1374T>C p.Gly458= synonymous_variant 12/261 NM_022763.4 P1Q53EP0-1

Frequencies

GnomAD3 genomes
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.512
AC:
77800
AN:
151908
Hom.:
20999
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.675
Gnomad AMI
AF:
0.445
Gnomad AMR
AF:
0.506
Gnomad ASJ
AF:
0.511
Gnomad EAS
AF:
0.513
Gnomad SAS
AF:
0.632
Gnomad FIN
AF:
0.469
Gnomad MID
AF:
0.582
Gnomad NFE
AF:
0.413
Gnomad OTH
AF:
0.519
GnomAD3 exomes
AF:
0.486
AC:
121463
AN:
249932
Hom.:
30534
AF XY:
0.489
AC XY:
66076
AN XY:
135164
show subpopulations
Gnomad AFR exome
AF:
0.671
Gnomad AMR exome
AF:
0.482
Gnomad ASJ exome
AF:
0.522
Gnomad EAS exome
AF:
0.551
Gnomad SAS exome
AF:
0.621
Gnomad FIN exome
AF:
0.451
Gnomad NFE exome
AF:
0.418
Gnomad OTH exome
AF:
0.474
GnomAD4 exome
AF:
0.439
AC:
641267
AN:
1459472
Hom.:
144815
Cov.:
40
AF XY:
0.444
AC XY:
322267
AN XY:
725898
show subpopulations
Gnomad4 AFR exome
AF:
0.681
Gnomad4 AMR exome
AF:
0.478
Gnomad4 ASJ exome
AF:
0.525
Gnomad4 EAS exome
AF:
0.482
Gnomad4 SAS exome
AF:
0.613
Gnomad4 FIN exome
AF:
0.446
Gnomad4 NFE exome
AF:
0.411
Gnomad4 OTH exome
AF:
0.473
GnomAD4 genome
?
    Genome Aggregation Database, over 76,156 genomes
AF:
0.512
AC:
77886
AN:
152028
Hom.:
21035
Cov.:
32
AF XY:
0.518
AC XY:
38482
AN XY:
74308
show subpopulations
Gnomad4 AFR
AF:
0.675
Gnomad4 AMR
AF:
0.506
Gnomad4 ASJ
AF:
0.511
Gnomad4 EAS
AF:
0.512
Gnomad4 SAS
AF:
0.629
Gnomad4 FIN
AF:
0.469
Gnomad4 NFE
AF:
0.413
Gnomad4 OTH
AF:
0.521
Alfa
AF:
0.439
Hom.:
25666
Bravo
AF:
0.521
Asia WGS
AF:
0.590
AC:
2053
AN:
3478
EpiCase
AF:
0.442
EpiControl
AF:
0.441

ClinVar

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

Submissions by phenotype

FNDC3B-related disorder Benign:1
Benign, criteria provided, single submitterclinical testingPreventionGenetics, part of Exact SciencesOct 30, 2019This variant is classified as benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.64
Cadd
Benign
7.3
Dann
Benign
0.65
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: rs2270568; hg19: chr3-172046861; COSMIC: COSV61039337; COSMIC: COSV61039337; API