Variant chr1-180787920-A-G details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_004736.4(XPR1):c.223+66A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.368 in 1,197,858 control chromosomes in the GnomAD database, including 84,086 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.32 ( 8274 hom., cov: 31)

Exomes 𝑓: 0.38 ( 75812 hom. )

Consequence

XPR1
NM_004736.4 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: 1.17

Variant links:

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]

XPR1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.81).

BP6

Variant 1-180787920-A-G is Benign according to our data. Variant chr1-180787920-A-G is described in ClinVar as [Benign]. Clinvar id is 1281131.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.379 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	MANE	Protein
XPR1	NM_004736.4 linkuse as main transcript	c.223+66A>G	intron_variant	ENST00000367590.9	NP_004727.2
XPR1	NM_001135669.2 linkuse as main transcript	c.223+66A>G	intron_variant		NP_001129141.1
XPR1	NM_001328662.2 linkuse as main transcript	c.223+66A>G	intron_variant		NP_001315591.1
XPR1	NR_137330.2 linkuse as main transcript	n.403+66A>G	intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
XPR1	ENST00000367590.9 linkuse as main transcript	c.223+66A>G		intron_variant		1	NM_004736.4	ENSP00000356562	P1	Q9UBH6-1
XPR1	ENST00000367589.3 linkuse as main transcript	c.223+66A>G		intron_variant		1		ENSP00000356561		Q9UBH6-2

Frequencies

GnomAD3 genomes

AF:

0.316

AC:

47898

AN:

151688

Hom.:

8270

Cov.:

show subpopulations

Gnomad AFR

AF:

0.184

Gnomad AMI

AF:

0.399

Gnomad AMR

AF:

0.335

Gnomad ASJ

AF:

0.342

Gnomad EAS

AF:

0.174

Gnomad SAS

AF:

0.339

Gnomad FIN

AF:

0.414

Gnomad MID

AF:

0.301

Gnomad NFE

AF:

0.383

Gnomad OTH

AF:

0.305

GnomAD4 exome

AF:

0.375

AC:

392766

AN:

1046052

Hom.:

75812

AF XY:

0.374

AC XY:

199499

AN XY:

533656

show subpopulations

Gnomad4 AFR exome

AF:

0.178

Gnomad4 AMR exome

AF:

0.308

Gnomad4 ASJ exome

AF:

0.336

Gnomad4 EAS exome

AF:

0.215

Gnomad4 SAS exome

AF:

0.346

Gnomad4 FIN exome

AF:

0.420

Gnomad4 NFE exome

AF:

0.395

Gnomad4 OTH exome

AF:

0.355

GnomAD4 genome

AF:

0.316

AC:

47909

AN:

151806

Hom.:

8274

Cov.:

AF XY:

0.317

AC XY:

23499

AN XY:

74160

show subpopulations

Gnomad4 AFR

AF:

0.184

Gnomad4 AMR

AF:

0.335

Gnomad4 ASJ

AF:

0.342

Gnomad4 EAS

AF:

0.174

Gnomad4 SAS

AF:

0.340

Gnomad4 FIN

AF:

0.414

Gnomad4 NFE

AF:

0.383

Gnomad4 OTH

AF:

0.301

Alfa

AF:

0.366

Hom.:

10292

Bravo

AF:

0.303

Asia WGS

AF:

0.289

AC:

1004

AN:

3476

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

not provided

Benign:2

Benign, criteria provided, single submitter	not provided	Breakthrough Genomics, Breakthrough Genomics	-	- -
Benign, criteria provided, single submitter	clinical testing	GeneDx	Jul 30, 2018	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.81

CADD

Benign

9.5

DANN

Benign

0.73

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.0

Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over