chr6-88929007-T-G
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_003800.5(RNGTT):āc.345A>Cā(p.Glu115Asp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000106 in 1,611,166 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 (ā ).
Frequency
Consequence
NM_003800.5 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/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RNGTT | NM_003800.5 | c.345A>C | p.Glu115Asp | missense_variant | 4/16 | ENST00000369485.9 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RNGTT | ENST00000369485.9 | c.345A>C | p.Glu115Asp | missense_variant | 4/16 | 1 | NM_003800.5 | P1 | |
RNGTT | ENST00000369475.7 | c.345A>C | p.Glu115Asp | missense_variant | 4/15 | 1 | |||
RNGTT | ENST00000538899.2 | c.345A>C | p.Glu115Asp | missense_variant | 4/12 | 1 | |||
RNGTT | ENST00000627296.1 | n.497A>C | non_coding_transcript_exon_variant | 4/14 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000200 AC: 5AN: 249822Hom.: 0 AF XY: 0.0000370 AC XY: 5AN XY: 135048
GnomAD4 exome AF: 0.00000959 AC: 14AN: 1459100Hom.: 0 Cov.: 30 AF XY: 0.00000964 AC XY: 7AN XY: 725804
GnomAD4 genome ? AF: 0.0000197 AC: 3AN: 152066Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74272
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jan 29, 2024 | The c.345A>C (p.E115D) alteration is located in exon 4 (coding exon 4) of the RNGTT gene. This alteration results from a A to C substitution at nucleotide position 345, causing the glutamic acid (E) at amino acid position 115 to be replaced by an aspartic acid (D). 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