14-85621596-T-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_013231.6(FLRT2):āc.82T>Gā(p.Ser28Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000378 in 1,614,048 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 ).
Frequency
Consequence
NM_013231.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FLRT2 | NM_013231.6 | c.82T>G | p.Ser28Ala | missense_variant | 2/2 | ENST00000330753.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FLRT2 | ENST00000330753.6 | c.82T>G | p.Ser28Ala | missense_variant | 2/2 | 1 | NM_013231.6 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152158Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000358 AC: 9AN: 251410Hom.: 0 AF XY: 0.0000294 AC XY: 4AN XY: 135866
GnomAD4 exome AF: 0.0000342 AC: 50AN: 1461890Hom.: 0 Cov.: 30 AF XY: 0.0000371 AC XY: 27AN XY: 727244
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152158Hom.: 0 Cov.: 32 AF XY: 0.0000807 AC XY: 6AN XY: 74320
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 22, 2022 | The c.82T>G (p.S28A) alteration is located in exon 2 (coding exon 1) of the FLRT2 gene. This alteration results from a T to G substitution at nucleotide position 82, causing the serine (S) at amino acid position 28 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