chr1-38911358-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_017821.5(RHBDL2):c.472C>T(p.Arg158Cys) variant causes a missense change. The variant allele was found at a frequency of 0.0000118 in 1,613,582 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R158H) has been classified as Uncertain significance.
Frequency
Consequence
NM_017821.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RHBDL2 | NM_017821.5 | c.472C>T | p.Arg158Cys | missense_variant | 4/8 | ENST00000372990.6 | |
RHBDL2 | NM_001304746.2 | c.712C>T | p.Arg238Cys | missense_variant | 4/8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RHBDL2 | ENST00000372990.6 | c.472C>T | p.Arg158Cys | missense_variant | 4/8 | 5 | NM_017821.5 | P1 | |
RRAGC-DT | ENST00000667635.1 | n.267+51119G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00000658 AC: 1AN: 151970Hom.: 0 Cov.: 31
GnomAD3 exomes AF: 0.0000437 AC: 11AN: 251476Hom.: 0 AF XY: 0.0000515 AC XY: 7AN XY: 135916
GnomAD4 exome AF: 0.0000123 AC: 18AN: 1461612Hom.: 0 Cov.: 30 AF XY: 0.0000179 AC XY: 13AN XY: 727140
GnomAD4 genome AF: 0.00000658 AC: 1AN: 151970Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 74224
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 13, 2021 | The c.472C>T (p.R158C) alteration is located in exon 4 (coding exon 3) of the RHBDL2 gene. This alteration results from a C to T substitution at nucleotide position 472, causing the arginine (R) at amino acid position 158 to be replaced by a cysteine (C). 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