rs201892348
Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 2P and 8B. PM2BP6_Very_Strong
The NM_021930.6(RINT1):c.2159G>A(p.Cys720Tyr) variant causes a missense change involving the alteration of a conserved nucleotide. The variant allele was found at a frequency of 0.0000515 in 1,610,564 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. C720F) has been classified as Likely benign.
Frequency
Consequence
NM_021930.6 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RINT1 | NM_021930.6 | c.2159G>A | p.Cys720Tyr | missense_variant | 14/15 | ENST00000257700.7 | |
EFCAB10 | NM_001355526.2 | c.*-174C>T | intron_variant | ENST00000480514.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RINT1 | ENST00000257700.7 | c.2159G>A | p.Cys720Tyr | missense_variant | 14/15 | 1 | NM_021930.6 | P1 | |
EFCAB10 | ENST00000480514.6 | c.*-174C>T | intron_variant | 1 | NM_001355526.2 | A2 |
Frequencies
GnomAD3 genomes AF: 0.0000723 AC: 11AN: 152112Hom.: 0 Cov.: 33
GnomAD3 exomes AF: 0.000112 AC: 28AN: 250630Hom.: 0 AF XY: 0.0000885 AC XY: 12AN XY: 135526
GnomAD4 exome AF: 0.0000494 AC: 72AN: 1458452Hom.: 0 Cov.: 29 AF XY: 0.0000455 AC XY: 33AN XY: 725774
GnomAD4 genome AF: 0.0000723 AC: 11AN: 152112Hom.: 0 Cov.: 33 AF XY: 0.0000808 AC XY: 6AN XY: 74300
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 20, 2020 | 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. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 07, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at