chr7-87382131-G-A
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_021151.4(CROT):c.1120G>A(p.Glu374Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000062 in 1,613,534 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_021151.4 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CROT | NM_021151.4 | c.1120G>A | p.Glu374Lys | missense_variant | 12/18 | ENST00000331536.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CROT | ENST00000331536.8 | c.1120G>A | p.Glu374Lys | missense_variant | 12/18 | 1 | NM_021151.4 | P1 | |
CROT | ENST00000419147.6 | c.1204G>A | p.Glu402Lys | missense_variant | 13/19 | 2 | |||
CROT | ENST00000442291.1 | c.1120G>A | p.Glu374Lys | missense_variant | 11/17 | 5 | |||
CROT | ENST00000479014.1 | n.325G>A | non_coding_transcript_exon_variant | 4/4 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000800 AC: 2AN: 250134Hom.: 0 AF XY: 0.0000148 AC XY: 2AN XY: 135274
GnomAD4 exome AF: 0.00000411 AC: 6AN: 1461404Hom.: 0 Cov.: 31 AF XY: 0.00000275 AC XY: 2AN XY: 727004
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.0000269 AC XY: 2AN XY: 74316
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 27, 2023 | The c.1204G>A (p.E402K) alteration is located in exon 13 (coding exon 11) of the CROT gene. This alteration results from a G to A substitution at nucleotide position 1204, causing the glutamic acid (E) at amino acid position 402 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