rs398124653
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4BS2
The NM_198391.3(FLRT3):c.205C>A(p.Gln69Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000533 in 1,613,610 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as risk factor (no stars).
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.205C>A | p.Gln69Lys | missense_variant | 3/3 | ENST00000341420.5 | |
MACROD2 | NM_001351661.2 | c.272-166177G>T | intron_variant | ENST00000684519.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLRT3 | ENST00000341420.5 | c.205C>A | p.Gln69Lys | missense_variant | 3/3 | 2 | NM_198391.3 | P1 | |
MACROD2 | ENST00000684519.1 | c.272-166177G>T | intron_variant | NM_001351661.2 | P2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152100Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000279 AC: 7AN: 250844Hom.: 0 AF XY: 0.0000369 AC XY: 5AN XY: 135552
GnomAD4 exome AF: 0.0000561 AC: 82AN: 1461510Hom.: 0 Cov.: 34 AF XY: 0.0000660 AC XY: 48AN XY: 727060
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152100Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74312
ClinVar
Submissions by phenotype
HYPOGONADOTROPIC HYPOGONADISM 21 WITH ANOSMIA, SUSCEPTIBILITY TO Other:1
risk factor, no assertion criteria provided | literature only | OMIM | May 02, 2013 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at