chr1-152515547-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate
The NM_019060.3(CRCT1):c.164C>T(p.Ser55Phe) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000188 in 1,593,770 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_019060.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CRCT1 | NM_019060.3 | c.164C>T | p.Ser55Phe | missense_variant | 2/2 | ENST00000368790.4 | |
CRCT1 | XM_011509656.3 | c.164C>T | p.Ser55Phe | missense_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CRCT1 | ENST00000368790.4 | c.164C>T | p.Ser55Phe | missense_variant | 2/2 | 1 | NM_019060.3 | P1 |
Frequencies
GnomAD3 genomes AF: 0.00000664 AC: 1AN: 150640Hom.: 0 Cov.: 34
GnomAD4 exome AF: 0.00000139 AC: 2AN: 1443130Hom.: 0 Cov.: 52 AF XY: 0.00000279 AC XY: 2AN XY: 717854
GnomAD4 genome AF: 0.00000664 AC: 1AN: 150640Hom.: 0 Cov.: 34 AF XY: 0.00 AC XY: 0AN XY: 73584
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Dec 13, 2023 | The c.164C>T (p.S55F) alteration is located in exon 2 (coding exon 1) of the CRCT1 gene. This alteration results from a C to T substitution at nucleotide position 164, causing the serine (S) at amino acid position 55 to be replaced by a phenylalanine (F). 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