9-129095408-C-G
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_000755.5(CRAT):āc.1870G>Cā(p.Ala624Pro) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0187 in 1,610,904 control chromosomes in the GnomAD database, including 1,181 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Likely benignin UniProt.
Frequency
Consequence
NM_000755.5 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -14 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRAT | NM_000755.5 | c.1870G>C | p.Ala624Pro | missense_variant | 14/14 | ENST00000318080.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRAT | ENST00000318080.7 | c.1870G>C | p.Ala624Pro | missense_variant | 14/14 | 1 | NM_000755.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0219 AC: 3338AN: 152142Hom.: 111 Cov.: 33
GnomAD3 exomes AF: 0.0423 AC: 10459AN: 247244Hom.: 749 AF XY: 0.0373 AC XY: 5014AN XY: 134438
GnomAD4 exome AF: 0.0184 AC: 26771AN: 1458644Hom.: 1070 Cov.: 32 AF XY: 0.0182 AC XY: 13185AN XY: 725712
GnomAD4 genome AF: 0.0220 AC: 3352AN: 152260Hom.: 111 Cov.: 33 AF XY: 0.0232 AC XY: 1727AN XY: 74454
ClinVar
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Jan 30, 2024 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at