chr1-180672654-A-T
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_004736.4(XPR1):c.70-9706A>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0393 in 152,284 control chromosomes in the GnomAD database, including 168 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.039 ( 168 hom., cov: 32)
Consequence
XPR1
NM_004736.4 intron
NM_004736.4 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.380
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=-0.64).
BS1
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0393 (5986/152284) while in subpopulation NFE AF= 0.0478 (3249/67990). AF 95% confidence interval is 0.0464. There are 168 homozygotes in gnomad4. There are 2922 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 5986 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
XPR1 | NM_004736.4 | c.70-9706A>T | intron_variant | ENST00000367590.9 | |||
XPR1 | NM_001135669.2 | c.70-9706A>T | intron_variant | ||||
XPR1 | NM_001328662.2 | c.70-9706A>T | intron_variant | ||||
XPR1 | NR_137330.2 | n.250-9706A>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
XPR1 | ENST00000367590.9 | c.70-9706A>T | intron_variant | 1 | NM_004736.4 | P1 | |||
XPR1 | ENST00000367589.3 | c.70-9706A>T | intron_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.0394 AC: 5988AN: 152166Hom.: 168 Cov.: 32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.0393 AC: 5986AN: 152284Hom.: 168 Cov.: 32 AF XY: 0.0392 AC XY: 2922AN XY: 74460
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ClinVar
Not reported inComputational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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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