NM_013280.5:c.186C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_013280.5(FLRT1):c.186C>T(p.Asn62Asn) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000889 in 1,461,744 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: not found (cov: 32)
Exomes 𝑓: 0.0000089 ( 0 hom. )
Consequence
FLRT1
NM_013280.5 synonymous
NM_013280.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.352
Publications
2 publications found
Genes affected
FLRT1 (HGNC:3760): (fibronectin leucine rich transmembrane protein 1) This gene encodes a member of the fibronectin leucine rich transmembrane protein (FLRT) family. The family members may function in cell adhesion and/or receptor signalling. Their protein structures resemble small leucine-rich proteoglycans found in the extracellular matrix. The encoded protein shares sequence similarity with two other family members, FLRT2 and FLRT3. This gene is expressed in kidney and brain. [provided by RefSeq, Jul 2008]
MACROD1 (HGNC:29598): (mono-ADP ribosylhydrolase 1) Enables ADP-ribosylglutamate hydrolase activity and deacetylase activity. Involved in cellular response to DNA damage stimulus; peptidyl-glutamate ADP-deribosylation; and purine nucleoside metabolic process. Located in nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
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ACMG classification
Classification was made for transcript
Our verdict: Likely_benign. The variant received -3 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 11-64116453-C-T is Benign according to our data. Variant chr11-64116453-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1563980.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.352 with no splicing effect.
Variant Effect in Transcripts
ACMG analysis was done for transcript: NM_013280.5. You can select a different transcript below to see updated ACMG assignments.
RefSeq Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FLRT1 | NM_013280.5 | MANE Select | c.186C>T | p.Asn62Asn | synonymous | Exon 3 of 3 | NP_037412.2 | ||
| MACROD1 | NM_014067.4 | MANE Select | c.517+34786G>A | intron | N/A | NP_054786.2 | |||
| FLRT1 | NM_001384466.1 | c.186C>T | p.Asn62Asn | synonymous | Exon 3 of 3 | NP_001371395.1 | Q9NZU1-2 |
Ensembl Transcripts
| Sel. | Gene | Transcript | Tags | HGVSc | HGVSp | Effect | Exon Rank | Protein | UniProt |
|---|---|---|---|---|---|---|---|---|---|
| FLRT1 | ENST00000682287.1 | MANE Select | c.186C>T | p.Asn62Asn | synonymous | Exon 3 of 3 | ENSP00000507207.1 | Q9NZU1-2 | |
| FLRT1 | ENST00000246841.3 | TSL:1 | c.186C>T | p.Asn62Asn | synonymous | Exon 2 of 2 | ENSP00000246841.3 | Q9NZU1-2 | |
| MACROD1 | ENST00000255681.7 | TSL:1 MANE Select | c.517+34786G>A | intron | N/A | ENSP00000255681.6 | Q9BQ69 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
32
GnomAD2 exomes AF: 0.0000120 AC: 3AN: 250000 AF XY: 0.00000739 show subpopulations
GnomAD2 exomes
AF:
AC:
3
AN:
250000
AF XY:
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome AF: 0.00000889 AC: 13AN: 1461744Hom.: 0 Cov.: 30 AF XY: 0.00000413 AC XY: 3AN XY: 727186 show subpopulations
GnomAD4 exome
AF:
AC:
13
AN:
1461744
Hom.:
Cov.:
30
AF XY:
AC XY:
3
AN XY:
727186
show subpopulations
African (AFR)
AF:
AC:
1
AN:
33480
American (AMR)
AF:
AC:
1
AN:
44724
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
3
AN:
39698
South Asian (SAS)
AF:
AC:
0
AN:
86258
European-Finnish (FIN)
AF:
AC:
0
AN:
53288
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
7
AN:
1112002
Other (OTH)
AF:
AC:
1
AN:
60390
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.456
Heterozygous variant carriers
0
1
2
3
4
5
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
0
2
4
6
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10
<30
30-35
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>80
Age
GnomAD4 genome
GnomAD4 genome
Cov.:
32
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
ClinVar submissions as Germline
View on ClinVar Significance:Likely benign
Revision:criteria provided, single submitter
Pathogenic
VUS
Benign
Condition
-
-
1
Peripheral neuropathy (1)
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
RBP_binding_hub_radar
RBP_regulation_power_radar
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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