NM_013280.5:c.123C>T
Variant names:
Variant summary
Our verdict is Likely benign. The variant received -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_013280.5(FLRT1):c.123C>T(p.Leu41Leu) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000274 in 1,461,558 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: 33)
Exomes 𝑓: 0.0000027 ( 0 hom. )
Consequence
FLRT1
NM_013280.5 synonymous
NM_013280.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.465
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 -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.61).
BP6
Variant 11-64116390-C-T is Benign according to our data. Variant chr11-64116390-C-T is described in ClinVar as Likely_benign. ClinVar VariationId is 1616138.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-0.465 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.123C>T | p.Leu41Leu | synonymous | Exon 3 of 3 | NP_037412.2 | ||
| MACROD1 | NM_014067.4 | MANE Select | c.517+34849G>A | intron | N/A | NP_054786.2 | |||
| FLRT1 | NM_001384466.1 | c.123C>T | p.Leu41Leu | 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.123C>T | p.Leu41Leu | synonymous | Exon 3 of 3 | ENSP00000507207.1 | Q9NZU1-2 | |
| FLRT1 | ENST00000246841.3 | TSL:1 | c.123C>T | p.Leu41Leu | synonymous | Exon 2 of 2 | ENSP00000246841.3 | Q9NZU1-2 | |
| MACROD1 | ENST00000255681.7 | TSL:1 MANE Select | c.517+34849G>A | intron | N/A | ENSP00000255681.6 | Q9BQ69 |
Frequencies
GnomAD3 genomes
GnomAD3 genomes
Cov.:
33
GnomAD2 exomes AF: 0.00000805 AC: 2AN: 248522 AF XY: 0.00 show subpopulations
GnomAD2 exomes
AF:
AC:
2
AN:
248522
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: 0.00000274 AC: 4AN: 1461558Hom.: 0 Cov.: 30 AF XY: 0.00000275 AC XY: 2AN XY: 727102 show subpopulations
GnomAD4 exome
AF:
AC:
4
AN:
1461558
Hom.:
Cov.:
30
AF XY:
AC XY:
2
AN XY:
727102
show subpopulations
African (AFR)
AF:
AC:
0
AN:
33474
American (AMR)
AF:
AC:
0
AN:
44714
Ashkenazi Jewish (ASJ)
AF:
AC:
0
AN:
26136
East Asian (EAS)
AF:
AC:
0
AN:
39700
South Asian (SAS)
AF:
AC:
0
AN:
86250
European-Finnish (FIN)
AF:
AC:
0
AN:
53154
Middle Eastern (MID)
AF:
AC:
0
AN:
5768
European-Non Finnish (NFE)
AF:
AC:
4
AN:
1111980
Other (OTH)
AF:
AC:
0
AN:
60382
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.475
Heterozygous variant carriers
0
1
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5
0.00
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0.60
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0.95
Allele balance
Age Distribution
Exome Het
Variant carriers
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Age
GnomAD4 genome
GnomAD4 genome
Cov.:
33
Alfa
AF:
Hom.:
Bravo
AF:
EpiCase
AF:
EpiControl
AF:
ClinVar
ClinVar submissions
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
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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