chr2-86986828-C-T
Variant summary
Our verdict is Likely benign. Variant got -1 ACMG points: 0P and 1B. BP4
The NM_001382344.1(RGPD1):c.3929C>T(p.Thr1310Ile) variant causes a missense change. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001382344.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -1 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RGPD1 | NM_001382344.1 | c.3929C>T | p.Thr1310Ile | missense_variant | Exon 20 of 23 | ENST00000641458.2 | NP_001369273.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RGPD1 | ENST00000641458.2 | c.3929C>T | p.Thr1310Ile | missense_variant | Exon 20 of 23 | NM_001382344.1 | ENSP00000492954.1 | |||
RGPD1 | ENST00000398193.8 | c.3929C>T | p.Thr1310Ile | missense_variant | Exon 20 of 23 | 1 | ENSP00000381253.3 | |||
RGPD1 | ENST00000428128.1 | n.*1848C>T | non_coding_transcript_exon_variant | Exon 7 of 10 | 1 | ENSP00000402729.1 | ||||
RGPD1 | ENST00000428128.1 | n.*1848C>T | 3_prime_UTR_variant | Exon 7 of 10 | 1 | ENSP00000402729.1 |
Frequencies
GnomAD3 genomes AF: 0.00 AC: 1AN: 78678Hom.: 0 Cov.: 10 FAILED QC
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000717 AC: 10AN: 1395426Hom.: 1 Cov.: 23 AF XY: 0.0000100 AC XY: 7AN XY: 698078
GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.0000127 AC: 1AN: 78678Hom.: 0 Cov.: 10 AF XY: 0.00 AC XY: 0AN XY: 36842
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.3905C>T (p.T1302I) alteration is located in exon 20 (coding exon 20) of the RGPD1 gene. This alteration results from a C to T substitution at nucleotide position 3905, causing the threonine (T) at amino acid position 1302 to be replaced by an isoleucine (I). 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