1-64009315-G-A
Variant summary
Our verdict is Likely benign. Variant got -3 ACMG points: 2P and 5B. PM2BP4_ModerateBP6_ModerateBP7
The NM_005012.4(ROR1):c.102G>A(p.Leu34=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000787 in 1,612,922 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00041 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000044 ( 0 hom. )
Consequence
ROR1
NM_005012.4 synonymous
NM_005012.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 1.27
Genes affected
ROR1 (HGNC:10256): (receptor tyrosine kinase like orphan receptor 1) This gene encodes a receptor tyrosine kinase-like orphan receptor that modulates neurite growth in the central nervous system. The encoded protein is a glycosylated type I membrane protein that belongs to the ROR subfamily of cell surface receptors. It is a pseudokinase that lacks catalytic activity and may interact with the non-canonical Wnt signalling pathway. This gene is highly expressed during early embryonic development but expressed at very low levels in adult tissues. Increased expression of this gene is associated with B-cell chronic lymphocytic leukaemia. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jun 2012]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -3 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
?
Variant 1-64009315-G-A is Benign according to our data. Variant chr1-64009315-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2713771.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=1.27 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROR1 | NM_005012.4 | c.102G>A | p.Leu34= | synonymous_variant | 2/9 | ENST00000371079.6 | |
ROR1 | NM_001083592.2 | c.102G>A | p.Leu34= | synonymous_variant | 2/7 | ||
ROR1 | XM_011541526.2 | c.-88G>A | 5_prime_UTR_variant | 2/9 | |||
ROR1 | XM_017001377.2 | c.-184G>A | 5_prime_UTR_variant | 1/10 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROR1 | ENST00000371079.6 | c.102G>A | p.Leu34= | synonymous_variant | 2/9 | 1 | NM_005012.4 | P1 | |
ROR1 | ENST00000371080.5 | c.102G>A | p.Leu34= | synonymous_variant | 2/7 | 1 | |||
ROR1 | ENST00000482426.1 | n.136G>A | non_coding_transcript_exon_variant | 2/6 | 5 |
Frequencies
GnomAD3 genomes ? AF: 0.000414 AC: 63AN: 152060Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.0000876 AC: 22AN: 251054Hom.: 0 AF XY: 0.0000811 AC XY: 11AN XY: 135672
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GnomAD4 exome AF: 0.0000438 AC: 64AN: 1460742Hom.: 0 Cov.: 29 AF XY: 0.0000344 AC XY: 25AN XY: 726768
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GnomAD4 genome ? AF: 0.000414 AC: 63AN: 152180Hom.: 0 Cov.: 32 AF XY: 0.000417 AC XY: 31AN XY: 74390
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Nov 02, 2022 | - - |
Computational scores
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Benign
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Benign
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at