8-23295975-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_001136108.3(R3HCC1):c.1201C>T(p.Arg401Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00016 in 1,549,580 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. R401H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001136108.3 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
R3HCC1 | NM_001136108.3 | c.1201C>T | p.Arg401Cys | missense_variant | Exon 8 of 8 | ENST00000265806.12 | NP_001129580.2 | |
R3HCC1 | NM_001301650.2 | c.1075C>T | p.Arg359Cys | missense_variant | Exon 9 of 9 | NP_001288579.1 | ||
R3HCC1 | NR_125897.1 | n.1170C>T | non_coding_transcript_exon_variant | Exon 9 of 9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
R3HCC1 | ENST00000265806.12 | c.1201C>T | p.Arg401Cys | missense_variant | Exon 8 of 8 | 1 | NM_001136108.3 | ENSP00000265806.8 |
Frequencies
GnomAD3 genomes AF: 0.000171 AC: 26AN: 152222Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000120 AC: 18AN: 150096Hom.: 0 AF XY: 0.000125 AC XY: 10AN XY: 80030
GnomAD4 exome AF: 0.000159 AC: 222AN: 1397240Hom.: 0 Cov.: 30 AF XY: 0.000177 AC XY: 122AN XY: 689114
GnomAD4 genome AF: 0.000171 AC: 26AN: 152340Hom.: 0 Cov.: 33 AF XY: 0.000134 AC XY: 10AN XY: 74488
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.640C>T (p.R214C) alteration is located in exon 8 (coding exon 5) of the R3HCC1 gene. This alteration results from a C to T substitution at nucleotide position 640, causing the arginine (R) at amino acid position 214 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