chr13-32171259-A-G
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4_StrongBP6_ModerateBS2
The NM_023037.3(FRY):c.2140A>G(p.Arg714Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000511 in 1,611,188 control chromosomes in the GnomAD database, including 11 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Consequence
NM_023037.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRY | NM_023037.3 | c.2140A>G | p.Arg714Gly | missense_variant | 18/61 | ENST00000542859.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRY | ENST00000542859.6 | c.2140A>G | p.Arg714Gly | missense_variant | 18/61 | 5 | NM_023037.3 | A1 | |
FRY | ENST00000647500.1 | c.2275A>G | p.Arg759Gly | missense_variant | 18/61 | ||||
FRY | ENST00000642040.1 | c.2140A>G | p.Arg714Gly | missense_variant | 18/62 | P4 | |||
FRY | ENST00000645780.1 | c.1990A>G | p.Arg664Gly | missense_variant | 19/62 |
Frequencies
GnomAD3 genomes ? AF: 0.00270 AC: 408AN: 151344Hom.: 6 Cov.: 32
GnomAD3 exomes AF: 0.000588 AC: 146AN: 248470Hom.: 1 AF XY: 0.000400 AC XY: 54AN XY: 134878
GnomAD4 exome AF: 0.000284 AC: 415AN: 1459740Hom.: 4 Cov.: 33 AF XY: 0.000233 AC XY: 169AN XY: 726366
GnomAD4 genome ? AF: 0.00269 AC: 408AN: 151448Hom.: 7 Cov.: 32 AF XY: 0.00281 AC XY: 208AN XY: 73978
ClinVar
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 24, 2017 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at