14-85622712-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013231.6(FLRT2):āc.1198C>Gā(p.Pro400Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000607 in 1,614,020 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 16/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā ). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P400L) has been classified as Uncertain significance.
Frequency
Consequence
NM_013231.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLRT2 | NM_013231.6 | c.1198C>G | p.Pro400Ala | missense_variant | 2/2 | ENST00000330753.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLRT2 | ENST00000330753.6 | c.1198C>G | p.Pro400Ala | missense_variant | 2/2 | 1 | NM_013231.6 | P1 | |
FLRT2 | ENST00000554746.1 | c.1198C>G | p.Pro400Ala | missense_variant | 2/2 | 1 | P1 | ||
FLRT2 | ENST00000682132.1 | c.1198C>G | p.Pro400Ala | missense_variant | 2/2 | P1 | |||
FLRT2 | ENST00000683129.1 | c.1198C>G | p.Pro400Ala | missense_variant | 2/2 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000318 AC: 8AN: 251400Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135876
GnomAD4 exome AF: 0.0000643 AC: 94AN: 1461866Hom.: 0 Cov.: 36 AF XY: 0.0000619 AC XY: 45AN XY: 727232
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152154Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74334
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 10, 2022 | The c.1198C>G (p.P400A) alteration is located in exon 2 (coding exon 1) of the FLRT2 gene. This alteration results from a C to G substitution at nucleotide position 1198, causing the proline (P) at amino acid position 400 to be replaced by an alanine (A). 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