rs561504020
Variant summary
Our verdict is Benign. The variant received -7 ACMG points: 1P and 8B. PP2BP4_StrongBS2
The NM_021244.5(RRAGD):c.1137G>C(p.Lys379Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000223 in 1,614,010 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021244.5 missense
Scores
Clinical Significance
Conservation
Publications
- hypomagnesemia 7, renal, with or without dilated cardiomyopathyInheritance: AD Classification: STRONG, MODERATE Submitted by: Ambry Genetics, Labcorp Genetics (formerly Invitae)
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ACMG classification
Our verdict: Benign. The variant received -7 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RRAGD | ENST00000369415.9 | c.1137G>C | p.Lys379Asn | missense_variant | Exon 7 of 7 | 1 | NM_021244.5 | ENSP00000358423.4 | ||
RRAGD | ENST00000359203.3 | c.684G>C | p.Lys228Asn | missense_variant | Exon 6 of 6 | 2 | ENSP00000352131.2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152140Hom.: 0 Cov.: 32 show subpopulations
GnomAD2 exomes AF: 0.0000517 AC: 13AN: 251228 AF XY: 0.0000589 show subpopulations
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461752Hom.: 0 Cov.: 31 AF XY: 0.0000179 AC XY: 13AN XY: 727194 show subpopulations
Age Distribution
GnomAD4 genome AF: 0.0000722 AC: 11AN: 152258Hom.: 0 Cov.: 32 AF XY: 0.000121 AC XY: 9AN XY: 74432 show subpopulations
Age Distribution
ClinVar
Submissions by phenotype
Inborn genetic diseases Uncertain:1
The c.1137G>C (p.K379N) alteration is located in exon 7 (coding exon 7) of the RRAGD gene. This alteration results from a G to C substitution at nucleotide position 1137, causing the lysine (K) at amino acid position 379 to be replaced by an asparagine (N). 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