X-106900793-C-T
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_ModerateBS2
The ENST00000276173.5(RIPPLY1):c.412G>A(p.Glu138Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000372 in 1,209,739 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 12 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
ENST00000276173.5 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RIPPLY1 | NM_138382.3 | c.412G>A | p.Glu138Lys | missense_variant | 4/4 | ENST00000276173.5 | NP_612391.1 | |
RIPPLY1 | NM_001171706.2 | c.271G>A | p.Glu91Lys | missense_variant | 2/2 | NP_001165177.1 | ||
CLDN2 | NM_001171092.1 | c.-179+289C>T | intron_variant | NP_001164563.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIPPLY1 | ENST00000276173.5 | c.412G>A | p.Glu138Lys | missense_variant | 4/4 | 1 | NM_138382.3 | ENSP00000276173 | P1 | |
RIPPLY1 | ENST00000411805.1 | c.271G>A | p.Glu91Lys | missense_variant | 2/2 | 1 | ENSP00000400539 | |||
CLDN2 | ENST00000541806.6 | c.-179+289C>T | intron_variant | 1 | ENSP00000441283 | P1 | ||||
MORC4 | ENST00000604604.1 | c.112-85007G>A | intron_variant | 2 | ENSP00000474750 |
Frequencies
GnomAD3 genomes AF: 0.0000625 AC: 7AN: 112016Hom.: 0 Cov.: 23 AF XY: 0.0000878 AC XY: 3AN XY: 34176
GnomAD3 exomes AF: 0.0000111 AC: 2AN: 180405Hom.: 0 AF XY: 0.0000301 AC XY: 2AN XY: 66533
GnomAD4 exome AF: 0.0000346 AC: 38AN: 1097723Hom.: 0 Cov.: 30 AF XY: 0.0000248 AC XY: 9AN XY: 363185
GnomAD4 genome AF: 0.0000625 AC: 7AN: 112016Hom.: 0 Cov.: 23 AF XY: 0.0000878 AC XY: 3AN XY: 34176
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 17, 2023 | The c.412G>A (p.E138K) alteration is located in exon 4 (coding exon 4) of the RIPPLY1 gene. This alteration results from a G to A substitution at nucleotide position 412, causing the glutamic acid (E) at amino acid position 138 to be replaced by a lysine (K). 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