chr20-14326378-C-T
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_198391.3(FLRT3):c.1129G>A(p.Ala377Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0117 in 1,613,912 control chromosomes in the GnomAD database, including 142 homozygotes. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another nucleotide change resulting in the same amino acid substitution has been previously reported as Likely benign in UniProt.
Frequency
Consequence
NM_198391.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0151 AC: 2290AN: 152106Hom.: 24 Cov.: 32
GnomAD3 exomes AF: 0.0110 AC: 2766AN: 250884Hom.: 37 AF XY: 0.0102 AC XY: 1377AN XY: 135562
GnomAD4 exome AF: 0.0113 AC: 16555AN: 1461688Hom.: 118 Cov.: 35 AF XY: 0.0111 AC XY: 8090AN XY: 727144
GnomAD4 genome AF: 0.0150 AC: 2289AN: 152224Hom.: 24 Cov.: 32 AF XY: 0.0149 AC XY: 1106AN XY: 74416
ClinVar
Submissions by phenotype
not provided Benign:5
Likely benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | Center for Pediatric Genomic Medicine, Children's Mercy Hospital and Clinics | Feb 11, 2016 | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 22, 2024 | - - |
Benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 18, 2021 | This variant is associated with the following publications: (PMID: 29767709) - |
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Nov 01, 2024 | FLRT3: BP4, BS1, BS2; MACROD2: BS1, BS2 - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at