chr1-180632070-G-A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_ModerateBP6_ModerateBA1
The NM_004736.4(XPR1):c.-132G>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 0.00682 in 1,048,498 control chromosomes in the GnomAD database, including 291 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.027 ( 188 hom., cov: 32)
Exomes 𝑓: 0.0033 ( 103 hom. )
Consequence
XPR1
NM_004736.4 5_prime_UTR
NM_004736.4 5_prime_UTR
Scores
1
1
Clinical Significance
Conservation
PhyloP100: 3.22
Genes affected
XPR1 (HGNC:12827): (xenotropic and polytropic retrovirus receptor 1) The protein encoded by this gene is a receptor for the xenotropic and polytropic classes of murine leukemia viruses. The encoded protein is involved in phosphate homeostasis by mediating phosphate export from the cell. Defects in this gene have been associated with idiopathic basal ganglia calcification-6. [provided by RefSeq, Jun 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.29).
BP6
?
Variant 1-180632070-G-A is Benign according to our data. Variant chr1-180632070-G-A is described in ClinVar as [Benign]. Clinvar id is 1258663.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0905 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPR1 | NM_004736.4 | c.-132G>A | 5_prime_UTR_variant | 1/15 | ENST00000367590.9 | ||
XPR1 | NM_001135669.2 | c.-132G>A | 5_prime_UTR_variant | 1/14 | |||
XPR1 | NM_001328662.2 | c.-132G>A | 5_prime_UTR_variant | 1/11 | |||
XPR1 | NR_137330.2 | n.49G>A | non_coding_transcript_exon_variant | 1/13 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPR1 | ENST00000367590.9 | c.-132G>A | 5_prime_UTR_variant | 1/15 | 1 | NM_004736.4 | P1 | ||
XPR1 | ENST00000367589.3 | c.-132G>A | 5_prime_UTR_variant | 1/14 | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.0274 AC: 4165AN: 152092Hom.: 189 Cov.: 32
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GnomAD4 exome AF: 0.00333 AC: 2983AN: 896288Hom.: 103 Cov.: 12 AF XY: 0.00282 AC XY: 1299AN XY: 460830
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GnomAD4 genome ? AF: 0.0274 AC: 4168AN: 152210Hom.: 188 Cov.: 32 AF XY: 0.0259 AC XY: 1931AN XY: 74424
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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 | Jul 17, 2018 | - - |
Computational scores
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Name
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Benign
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Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at