chr20-14325601-A-G
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_198391.3(FLRT3):c.1906T>C(p.Tyr636His) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000347 in 1,613,384 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Y636C) has been classified as Uncertain significance.
Frequency
Consequence
NM_198391.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLRT3 | NM_198391.3 | c.1906T>C | p.Tyr636His | missense_variant | 3/3 | ENST00000341420.5 | |
MACROD2 | NM_001351661.2 | c.272-167878A>G | intron_variant | ENST00000684519.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLRT3 | ENST00000341420.5 | c.1906T>C | p.Tyr636His | missense_variant | 3/3 | 2 | NM_198391.3 | P1 | |
MACROD2 | ENST00000684519.1 | c.272-167878A>G | intron_variant | NM_001351661.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000131 AC: 2AN: 152142Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000104 AC: 26AN: 250626Hom.: 1 AF XY: 0.000148 AC XY: 20AN XY: 135466
GnomAD4 exome AF: 0.0000370 AC: 54AN: 1461124Hom.: 1 Cov.: 30 AF XY: 0.0000523 AC XY: 38AN XY: 726866
GnomAD4 genome ? AF: 0.0000131 AC: 2AN: 152260Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74440
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 22, 2024 | The c.1906T>C (p.Y636H) alteration is located in exon 3 (coding exon 1) of the FLRT3 gene. This alteration results from a T to C substitution at nucleotide position 1906, causing the tyrosine (Y) at amino acid position 636 to be replaced by a histidine (H). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at