6-88929017-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003800.5(RNGTT):c.335G>A(p.Arg112Gln) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000329 in 1,612,040 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_003800.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RNGTT | NM_003800.5 | c.335G>A | p.Arg112Gln | missense_variant | 4/16 | ENST00000369485.9 | NP_003791.3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RNGTT | ENST00000369485.9 | c.335G>A | p.Arg112Gln | missense_variant | 4/16 | 1 | NM_003800.5 | ENSP00000358497 | P1 | |
RNGTT | ENST00000369475.7 | c.335G>A | p.Arg112Gln | missense_variant | 4/15 | 1 | ENSP00000358487 | |||
RNGTT | ENST00000538899.2 | c.335G>A | p.Arg112Gln | missense_variant | 4/12 | 1 | ENSP00000442609 | |||
RNGTT | ENST00000627296.1 | n.487G>A | non_coding_transcript_exon_variant | 4/14 | 2 |
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 151860Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000160 AC: 4AN: 250574Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135428
GnomAD4 exome AF: 0.0000336 AC: 49AN: 1460180Hom.: 0 Cov.: 30 AF XY: 0.0000358 AC XY: 26AN XY: 726354
GnomAD4 genome AF: 0.0000263 AC: 4AN: 151860Hom.: 0 Cov.: 32 AF XY: 0.0000539 AC XY: 4AN XY: 74162
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Mar 26, 2024 | The c.335G>A (p.R112Q) alteration is located in exon 4 (coding exon 4) of the RNGTT gene. This alteration results from a G to A substitution at nucleotide position 335, causing the arginine (R) at amino acid position 112 to be replaced by a glutamine (Q). 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