chr1-204155090-C-T
Variant summary
Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.
The NM_000537.4(REN):c.1147G>A(p.Ala383Thr) variant causes a missense change. The variant allele was found at a frequency of 0.00000372 in 1,614,106 control chromosomes in the GnomAD database, with no homozygous occurrence. 13/22 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_000537.4 missense
Scores
Clinical Significance
Conservation
Publications
- familial juvenile hyperuricemic nephropathy type 2Inheritance: AD Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, Ambry Genetics, Labcorp Genetics (formerly Invitae), ClinGen
- renal tubular dysgenesis of genetic originInheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Orphanet, Ambry Genetics
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ACMG classification
Our verdict: Uncertain_significance. The variant received 0 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
REN | ENST00000272190.9 | c.1147G>A | p.Ala383Thr | missense_variant | Exon 10 of 10 | 1 | NM_000537.4 | ENSP00000272190.8 | ||
REN | ENST00000638118.1 | c.1033G>A | p.Ala345Thr | missense_variant | Exon 12 of 12 | 5 | ENSP00000490307.1 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 33 show subpopulations
GnomAD2 exomes AF: 0.00000802 AC: 2AN: 249222 AF XY: 0.0000148 show subpopulations
GnomAD4 exome AF: 0.00000274 AC: 4AN: 1461860Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727230 show subpopulations
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152246Hom.: 0 Cov.: 33 AF XY: 0.00 AC XY: 0AN XY: 74380 show subpopulations
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1147G>A (p.A383T) alteration is located in exon 10 (coding exon 10) of the REN gene. This alteration results from a G to A substitution at nucleotide position 1147, causing the alanine (A) at amino acid position 383 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