14-85622560-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_013231.6(FLRT2):c.1046C>T(p.Ala349Val) variant causes a missense change. The variant allele was found at a frequency of 0.000026 in 1,613,648 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 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
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
FLRT2 | ENST00000330753.6 | c.1046C>T | p.Ala349Val | missense_variant | Exon 2 of 2 | 1 | NM_013231.6 | ENSP00000332879.4 | ||
FLRT2 | ENST00000554746.1 | c.1046C>T | p.Ala349Val | missense_variant | Exon 2 of 2 | 1 | ENSP00000451050.1 | |||
FLRT2 | ENST00000682132.1 | c.1046C>T | p.Ala349Val | missense_variant | Exon 2 of 2 | ENSP00000507088.1 | ||||
FLRT2 | ENST00000683129.1 | c.1046C>T | p.Ala349Val | missense_variant | Exon 2 of 2 | ENSP00000507815.1 |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000797 AC: 2AN: 250978Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135656
GnomAD4 exome AF: 0.0000281 AC: 41AN: 1461626Hom.: 0 Cov.: 37 AF XY: 0.0000344 AC XY: 25AN XY: 727124
GnomAD4 genome AF: 0.00000658 AC: 1AN: 152022Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74262
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1046C>T (p.A349V) alteration is located in exon 2 (coding exon 1) of the FLRT2 gene. This alteration results from a C to T substitution at nucleotide position 1046, causing the alanine (A) at amino acid position 349 to be replaced by a valine (V). 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