chr1-63774394-G-A
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_005012.4(ROR1):c.-24G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00383 in 1,255,210 control chromosomes in the GnomAD database, including 158 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.020 ( 103 hom., cov: 32)
Exomes 𝑓: 0.0017 ( 55 hom. )
Consequence
ROR1
NM_005012.4 5_prime_UTR
NM_005012.4 5_prime_UTR
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.724
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 Benign. Variant got -14 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.52).
BP6
?
Variant 1-63774394-G-A is Benign according to our data. Variant chr1-63774394-G-A is described in ClinVar as [Benign]. Clinvar id is 1235539.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0661 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
ROR1 | NM_005012.4 | c.-24G>A | 5_prime_UTR_variant | 1/9 | ENST00000371079.6 | ||
ROR1 | NM_001083592.2 | c.-24G>A | 5_prime_UTR_variant | 1/7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ROR1 | ENST00000371079.6 | c.-24G>A | 5_prime_UTR_variant | 1/9 | 1 | NM_005012.4 | P1 | ||
ROR1 | ENST00000371080.5 | c.-24G>A | 5_prime_UTR_variant | 1/7 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0197 AC: 2977AN: 151280Hom.: 104 Cov.: 32
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GnomAD3 exomes AF: 0.00148 AC: 44AN: 29784Hom.: 1 AF XY: 0.00133 AC XY: 24AN XY: 18058
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GnomAD4 exome AF: 0.00166 AC: 1832AN: 1103822Hom.: 55 Cov.: 23 AF XY: 0.00147 AC XY: 789AN XY: 538230
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GnomAD4 genome ? AF: 0.0197 AC: 2978AN: 151388Hom.: 103 Cov.: 32 AF XY: 0.0189 AC XY: 1400AN XY: 73984
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | May 22, 2021 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
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