chr11-64118100-C-T
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_013280.5(FLRT1):c.1833C>T(p.Ile611=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00738 in 1,611,510 control chromosomes in the GnomAD database, including 59 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★). Synonymous variant affecting the same amino acid position (i.e. I611I) has been classified as Benign.
Frequency
Consequence
NM_013280.5 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLRT1 | NM_013280.5 | c.1833C>T | p.Ile611= | synonymous_variant | 3/3 | ENST00000682287.1 | |
MACROD1 | NM_014067.4 | c.517+33139G>A | intron_variant | ENST00000255681.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLRT1 | ENST00000682287.1 | c.1833C>T | p.Ile611= | synonymous_variant | 3/3 | NM_013280.5 | P1 | ||
MACROD1 | ENST00000255681.7 | c.517+33139G>A | intron_variant | 1 | NM_014067.4 | P4 |
Frequencies
GnomAD3 genomes AF: 0.00638 AC: 972AN: 152248Hom.: 4 Cov.: 34
GnomAD3 exomes AF: 0.00653 AC: 1635AN: 250538Hom.: 9 AF XY: 0.00685 AC XY: 928AN XY: 135486
GnomAD4 exome AF: 0.00748 AC: 10921AN: 1459144Hom.: 55 Cov.: 89 AF XY: 0.00737 AC XY: 5343AN XY: 725360
GnomAD4 genome AF: 0.00638 AC: 972AN: 152366Hom.: 4 Cov.: 34 AF XY: 0.00682 AC XY: 508AN XY: 74520
ClinVar
Submissions by phenotype
Peripheral neuropathy Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Aug 04, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at