chr4-37634921-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_001085400.2(RELL1):c.646C>T(p.Arg216Cys) variant causes a missense change. The variant allele was found at a frequency of 0.00000342 in 1,461,894 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. R216H) has been classified as Uncertain significance.
Frequency
Consequence
NM_001085400.2 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 |
---|---|---|---|---|---|---|---|
RELL1 | NM_001085400.2 | c.646C>T | p.Arg216Cys | missense_variant | 5/7 | ENST00000454158.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RELL1 | ENST00000454158.7 | c.646C>T | p.Arg216Cys | missense_variant | 5/7 | 5 | NM_001085400.2 | P1 | |
RELL1 | ENST00000314117.8 | c.646C>T | p.Arg216Cys | missense_variant | 5/7 | 1 | P1 | ||
RELL1 | ENST00000512114.1 | c.709C>T | p.Arg237Cys | missense_variant | 5/5 | 3 |
Frequencies
GnomAD3 genomes ? Cov.: 33
GnomAD3 exomes AF: 0.00000801 AC: 2AN: 249568Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135400
GnomAD4 exome AF: 0.00000342 AC: 5AN: 1461894Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 727248
GnomAD4 genome ? Cov.: 33
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 15, 2023 | The c.646C>T (p.R216C) alteration is located in exon 5 (coding exon 5) of the RELL1 gene. This alteration results from a C to T substitution at nucleotide position 646, causing the arginine (R) at amino acid position 216 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