chr7-87361460-C-T
Variant summary
Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_021151.4(CROT):c.311C>T(p.Ala104Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000595 in 1,613,584 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 14/21 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
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ACMG classification
Verdict is Likely_benign. Variant got -2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CROT | NM_021151.4 | c.311C>T | p.Ala104Val | missense_variant | 5/18 | ENST00000331536.8 | |
CROT | NM_001143935.2 | c.395C>T | p.Ala132Val | missense_variant | 6/19 | ||
CROT | XM_011516337.4 | c.311C>T | p.Ala104Val | missense_variant | 5/18 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CROT | ENST00000331536.8 | c.311C>T | p.Ala104Val | missense_variant | 5/18 | 1 | NM_021151.4 | P1 | |
CROT | ENST00000419147.6 | c.395C>T | p.Ala132Val | missense_variant | 6/19 | 2 | |||
CROT | ENST00000442291.1 | c.311C>T | p.Ala104Val | missense_variant | 4/17 | 5 | |||
CROT | ENST00000488850.1 | n.18C>T | non_coding_transcript_exon_variant | 1/3 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0000329 AC: 5AN: 152050Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.000119 AC: 30AN: 251198Hom.: 0 AF XY: 0.000162 AC XY: 22AN XY: 135784
GnomAD4 exome AF: 0.0000623 AC: 91AN: 1461534Hom.: 0 Cov.: 31 AF XY: 0.0000894 AC XY: 65AN XY: 727080
GnomAD4 genome ? AF: 0.0000329 AC: 5AN: 152050Hom.: 0 Cov.: 32 AF XY: 0.0000135 AC XY: 1AN XY: 74284
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 12, 2023 | The c.395C>T (p.A132V) alteration is located in exon 6 (coding exon 4) of the CROT gene. This alteration results from a C to T substitution at nucleotide position 395, causing the alanine (A) at amino acid position 132 to be replaced by a valine (V). 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