chr5-76618204-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_004101.4(F2RL2):c.503C>A(p.Ala168Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000675 in 1,614,180 control chromosomes in the GnomAD database, with no homozygous occurrence. 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. A168G) has been classified as Uncertain significance.
Frequency
Consequence
NM_004101.4 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 |
---|---|---|---|---|---|---|---|
F2RL2 | NM_004101.4 | c.503C>A | p.Ala168Asp | missense_variant | 2/2 | ENST00000296641.5 | |
IQGAP2 | NM_006633.5 | c.1521+7021G>T | intron_variant | ENST00000274364.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
F2RL2 | ENST00000296641.5 | c.503C>A | p.Ala168Asp | missense_variant | 2/2 | 1 | NM_004101.4 | P2 | |
IQGAP2 | ENST00000274364.11 | c.1521+7021G>T | intron_variant | 1 | NM_006633.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000460 AC: 70AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000637 AC: 16AN: 250984Hom.: 0 AF XY: 0.0000442 AC XY: 6AN XY: 135700
GnomAD4 exome AF: 0.0000267 AC: 39AN: 1461872Hom.: 0 Cov.: 33 AF XY: 0.0000234 AC XY: 17AN XY: 727232
GnomAD4 genome ? AF: 0.000460 AC: 70AN: 152308Hom.: 0 Cov.: 32 AF XY: 0.000336 AC XY: 25AN XY: 74468
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 06, 2021 | The c.503C>A (p.A168D) alteration is located in exon 2 (coding exon 2) of the F2RL2 gene. This alteration results from a C to A substitution at nucleotide position 503, causing the alanine (A) at amino acid position 168 to be replaced by an aspartic acid (D). 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