2-182838416-G-A
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BS2
The NM_001463.4(FRZB):c.790C>T(p.Arg264Cys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.00012 in 1,609,332 control chromosomes in the GnomAD database, including 1 homozygotes. 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. R264H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001463.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FRZB | NM_001463.4 | c.790C>T | p.Arg264Cys | missense_variant | 4/6 | ENST00000295113.5 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FRZB | ENST00000295113.5 | c.790C>T | p.Arg264Cys | missense_variant | 4/6 | 1 | NM_001463.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.000132 AC: 20AN: 151962Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000152 AC: 38AN: 250390Hom.: 0 AF XY: 0.000163 AC XY: 22AN XY: 135312
GnomAD4 exome AF: 0.000119 AC: 173AN: 1457252Hom.: 1 Cov.: 31 AF XY: 0.000123 AC XY: 89AN XY: 725176
GnomAD4 genome ? AF: 0.000132 AC: 20AN: 152080Hom.: 0 Cov.: 32 AF XY: 0.000108 AC XY: 8AN XY: 74358
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Feb 01, 2023 | The c.790C>T (p.R264C) alteration is located in exon 4 (coding exon 4) of the FRZB gene. This alteration results from a C to T substitution at nucleotide position 790, causing the arginine (R) at amino acid position 264 to be replaced by a cysteine (C). 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