20-50595377-A-G
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001290268.2(RIPOR3):c.2042T>C(p.Ile681Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,613,886 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001290268.2 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 |
---|---|---|---|---|---|---|---|
RIPOR3 | NM_001290268.2 | c.2042T>C | p.Ile681Thr | missense_variant | 16/22 | ENST00000327979.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RIPOR3 | ENST00000327979.8 | c.2042T>C | p.Ile681Thr | missense_variant | 16/22 | 2 | NM_001290268.2 | ||
RIPOR3 | ENST00000045083.6 | c.2030T>C | p.Ile677Thr | missense_variant | 16/22 | 5 | P1 | ||
RIPOR3 | ENST00000488529.5 | n.282T>C | non_coding_transcript_exon_variant | 3/7 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152136Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000281 AC: 7AN: 249536Hom.: 0 AF XY: 0.0000295 AC XY: 4AN XY: 135382
GnomAD4 exome AF: 0.0000219 AC: 32AN: 1461632Hom.: 0 Cov.: 30 AF XY: 0.0000165 AC XY: 12AN XY: 727106
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152254Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74446
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 26, 2023 | The c.2030T>C (p.I677T) alteration is located in exon 16 (coding exon 15) of the FAM65C gene. This alteration results from a T to C substitution at nucleotide position 2030, causing the isoleucine (I) at amino acid position 677 to be replaced by a threonine (T). 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