9-5335408-C-T
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_006911.4(RLN1):c.401G>A(p.Arg134His) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000384 in 1,613,456 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 Likely benign (★).
Frequency
Consequence
NM_006911.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RLN1 | NM_006911.4 | c.401G>A | p.Arg134His | missense_variant | 2/2 | ENST00000223862.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RLN1 | ENST00000223862.2 | c.401G>A | p.Arg134His | missense_variant | 2/2 | 1 | NM_006911.4 | P1 | |
RLN1 | ENST00000487557.2 | n.325G>A | non_coding_transcript_exon_variant | 2/2 | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.000191 AC: 29AN: 151866Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000756 AC: 19AN: 251384Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135864
GnomAD4 exome AF: 0.0000226 AC: 33AN: 1461590Hom.: 0 Cov.: 31 AF XY: 0.0000206 AC XY: 15AN XY: 727100
GnomAD4 genome ? AF: 0.000191 AC: 29AN: 151866Hom.: 0 Cov.: 32 AF XY: 0.000175 AC XY: 13AN XY: 74136
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | May 09, 2023 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at