rs61729285
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_StrongBS1_Supporting
The NM_012232.6(CAVIN1):c.65C>T(p.Pro22Leu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0002 in 1,611,430 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. 14/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_012232.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CAVIN1 | NM_012232.6 | c.65C>T | p.Pro22Leu | missense_variant | 1/2 | ENST00000357037.6 | NP_036364.2 | |
CAVIN1 | XM_005257242.5 | c.65C>T | p.Pro22Leu | missense_variant | 1/2 | XP_005257299.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CAVIN1 | ENST00000357037.6 | c.65C>T | p.Pro22Leu | missense_variant | 1/2 | 1 | NM_012232.6 | ENSP00000349541.4 |
Frequencies
GnomAD3 genomes AF: 0.000986 AC: 150AN: 152152Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000217 AC: 52AN: 239818Hom.: 0 AF XY: 0.000167 AC XY: 22AN XY: 131690
GnomAD4 exome AF: 0.000115 AC: 168AN: 1459160Hom.: 1 Cov.: 32 AF XY: 0.000103 AC XY: 75AN XY: 725840
GnomAD4 genome AF: 0.00101 AC: 154AN: 152270Hom.: 0 Cov.: 32 AF XY: 0.000967 AC XY: 72AN XY: 74466
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Sep 29, 2023 | The c.65C>T (p.P22L) alteration is located in exon 1 (coding exon 1) of the PTRF gene. This alteration results from a C to T substitution at nucleotide position 65, causing the proline (P) at amino acid position 22 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. - |
Monogenic diabetes Uncertain:1
Uncertain significance, criteria provided, single submitter | research | Personalized Diabetes Medicine Program, University of Maryland School of Medicine | Feb 17, 2017 | ACMG Criteria:BP4 (9 predictors) - |
Congenital generalized lipodystrophy type 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Feb 19, 2020 | - - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Dec 31, 2019 | - - |
CAVIN1-related disorder Benign:1
Likely benign, no assertion criteria provided | clinical testing | PreventionGenetics, part of Exact Sciences | Oct 27, 2020 | This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at