chr7-87382123-T-C
Variant summary
Our verdict is Likely benign. Variant got -4 ACMG points: 2P and 6B. PM2BP4_StrongBP6_Moderate
The NM_021151.4(CROT):āc.1112T>Cā(p.Ile371Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000397 in 1,613,576 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Consequence
NM_021151.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Likely_benign. Variant got -4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CROT | NM_021151.4 | c.1112T>C | p.Ile371Thr | missense_variant | 12/18 | ENST00000331536.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CROT | ENST00000331536.8 | c.1112T>C | p.Ile371Thr | missense_variant | 12/18 | 1 | NM_021151.4 | P1 | |
CROT | ENST00000419147.6 | c.1196T>C | p.Ile399Thr | missense_variant | 13/19 | 2 | |||
CROT | ENST00000442291.1 | c.1112T>C | p.Ile371Thr | missense_variant | 11/17 | 5 | |||
CROT | ENST00000479014.1 | n.317T>C | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes AF: 0.000191 AC: 29AN: 152190Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000480 AC: 12AN: 250122Hom.: 0 AF XY: 0.0000444 AC XY: 6AN XY: 135260
GnomAD4 exome AF: 0.0000239 AC: 35AN: 1461386Hom.: 0 Cov.: 31 AF XY: 0.0000220 AC XY: 16AN XY: 727000
GnomAD4 genome AF: 0.000191 AC: 29AN: 152190Hom.: 0 Cov.: 32 AF XY: 0.000215 AC XY: 16AN XY: 74354
ClinVar
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 27, 2022 | 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at