20-14325600-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_198391.3(FLRT3):āc.1907A>Gā(p.Tyr636Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000186 in 1,613,252 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (ā ).
Frequency
Consequence
NM_198391.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLRT3 | ENST00000341420.5 | c.1907A>G | p.Tyr636Cys | missense_variant | Exon 3 of 3 | 2 | NM_198391.3 | ENSP00000339912.4 | ||
MACROD2 | ENST00000684519.1 | c.272-167879T>C | intron_variant | Intron 3 of 17 | NM_001351661.2 | ENSP00000507484.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000399 AC: 1AN: 250616Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135448
GnomAD4 exome AF: 0.0000192 AC: 28AN: 1461084Hom.: 0 Cov.: 30 AF XY: 0.0000138 AC XY: 10AN XY: 726832
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152168Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74332
ClinVar
Submissions by phenotype
not provided Uncertain:1
This sequence change replaces tyrosine, which is neutral and polar, with cysteine, which is neutral and slightly polar, at codon 636 of the FLRT3 protein (p.Tyr636Cys). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with FLRT3-related conditions. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at