6-24818557-A-G
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BA1
The NM_001286445.3(RIPOR2):c.2937T>C(p.Ala979Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.33 in 1,547,186 control chromosomes in the GnomAD database, including 89,341 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Consequence
NM_001286445.3 synonymous
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -21 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
RIPOR2 | NM_001286445.3 | c.2937T>C | p.Ala979Ala | synonymous_variant | Exon 20 of 22 | ENST00000643898.2 | NP_001273374.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
RIPOR2 | ENST00000643898.2 | c.2937T>C | p.Ala979Ala | synonymous_variant | Exon 20 of 22 | NM_001286445.3 | ENSP00000494268.2 | |||
RIPOR2 | ENST00000259698.9 | c.3000T>C | p.Ala1000Ala | synonymous_variant | Exon 21 of 23 | 1 | ENSP00000259698.4 | |||
RIPOR2 | ENST00000613507.4 | c.3000T>C | p.Ala1000Ala | synonymous_variant | Exon 21 of 23 | 5 | ENSP00000482957.1 | |||
RIPOR2 | ENST00000538035.6 | c.2850T>C | p.Ala950Ala | synonymous_variant | Exon 20 of 22 | 2 | ENSP00000441138.2 |
Frequencies
GnomAD3 genomes AF: 0.306 AC: 46460AN: 151866Hom.: 8017 Cov.: 30
GnomAD3 exomes AF: 0.378 AC: 59163AN: 156506Hom.: 12350 AF XY: 0.379 AC XY: 31371AN XY: 82800
GnomAD4 exome AF: 0.332 AC: 463697AN: 1395202Hom.: 81318 Cov.: 31 AF XY: 0.336 AC XY: 231096AN XY: 688286
GnomAD4 genome AF: 0.306 AC: 46500AN: 151984Hom.: 8023 Cov.: 30 AF XY: 0.315 AC XY: 23385AN XY: 74256
ClinVar
Submissions by phenotype
not specified Benign:2
p.Ala1000Ala in exon 21 of FAM65B: This variant is not expected to have clinical significance because it does not alter an amino acid residue, is not located wi thin the splice consensus sequence, and has been identified in 67.95% (424/624) of East Asian chromosomes by the Exome Aggregation Consortium (ExAC, http://exac .broadinstitute.org; dbSNP rs9358802). -
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
not provided Benign:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at