1-64009337-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP2BP4
The NM_005012.4(ROR1):c.124C>T(p.Pro42Ser) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P42L) has been classified as Uncertain significance.
Frequency
Consequence
NM_005012.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROR1 | NM_005012.4 | c.124C>T | p.Pro42Ser | missense_variant | 2/9 | ENST00000371079.6 | |
ROR1 | NM_001083592.2 | c.124C>T | p.Pro42Ser | missense_variant | 2/7 | ||
ROR1 | XM_011541526.2 | c.-66C>T | 5_prime_UTR_variant | 2/9 | |||
ROR1 | XM_017001377.2 | c.-162C>T | 5_prime_UTR_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROR1 | ENST00000371079.6 | c.124C>T | p.Pro42Ser | missense_variant | 2/9 | 1 | NM_005012.4 | P1 | |
ROR1 | ENST00000371080.5 | c.124C>T | p.Pro42Ser | missense_variant | 2/7 | 1 | |||
ROR1 | ENST00000482426.1 | n.158C>T | non_coding_transcript_exon_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome Cov.: 29
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 23, 2023 | The c.124C>T (p.P42S) alteration is located in exon 2 (coding exon 2) of the ROR1 gene. This alteration results from a C to T substitution at nucleotide position 124, causing the proline (P) at amino acid position 42 to be replaced by a serine (S). 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
Publications
No publications associated with this variant yet.