11-64116552-C-T
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_013280.5(FLRT1):c.285C>T(p.Asn95=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,614,076 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: 𝑓 0.000053 ( 0 hom., cov: 33)
Exomes 𝑓: 0.000033 ( 0 hom. )
Consequence
FLRT1
NM_013280.5 synonymous
NM_013280.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -2.29
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 made for transcript
Verdict is Likely_benign. Variant got -5 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.51).
BP6
Variant 11-64116552-C-T is Benign according to our data. Variant chr11-64116552-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 1128795.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=-2.29 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FLRT1 | NM_013280.5 | c.285C>T | p.Asn95= | synonymous_variant | 3/3 | ENST00000682287.1 | NP_037412.2 | |
MACROD1 | NM_014067.4 | c.517+34687G>A | intron_variant | ENST00000255681.7 | NP_054786.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLRT1 | ENST00000682287.1 | c.285C>T | p.Asn95= | synonymous_variant | 3/3 | NM_013280.5 | ENSP00000507207 | P1 | ||
MACROD1 | ENST00000255681.7 | c.517+34687G>A | intron_variant | 1 | NM_014067.4 | ENSP00000255681 | P4 |
Frequencies
GnomAD3 genomes AF: 0.0000526 AC: 8AN: 152184Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251302Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135872
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GnomAD4 exome AF: 0.0000328 AC: 48AN: 1461774Hom.: 0 Cov.: 69 AF XY: 0.0000371 AC XY: 27AN XY: 727184
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GnomAD4 genome AF: 0.0000525 AC: 8AN: 152302Hom.: 0 Cov.: 33 AF XY: 0.0000806 AC XY: 6AN XY: 74466
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
Peripheral neuropathy Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Oct 28, 2020 | - - |
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
RBP_binding_hub_radar
RBP_regulation_power_radar
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at