Variant chrX-102714234-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_001004051.4(GPRASP2):c.-366A>G variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.114 in 111,396 control chromosomes in the GnomAD database, including 658 homozygotes. There are 3,612 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.11 ( 657 hom., 3607 hem., cov: 23)

Exomes 𝑓: 0.055 ( 1 hom. 5 hem. )

Consequence

GPRASP2
NM_001004051.4 5_prime_UTR

Scores

Clinical Significance

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

Conservation

PhyloP100: -0.0490

Variant links:

Genes affected

GPRASP2 (HGNC:25169): (G protein-coupled receptor associated sorting protein 2) The protein encoded by this gene is a member of a family that regulates the activity of G protein-coupled receptors (GPCRs). The encoded protein has been shown to be capable of interacting with several GPCRs, including the M1 muscarinic acetylcholine receptor and the calcitonin receptor. Several transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, May 2010]

GPRASP2 links:

ARMCX5-GPRASP2 (HGNC:42000): (ARMCX5-GPRASP2 readthrough) This locus represents naturally occurring readthrough transcription among the adjacent armadillo repeat containing, X-linked 5 (ARMCX5), G protein-coupled receptor associated sorting proteins 1 and 2 (GPRASP1 and GPRASP2), basic helix-loop-helix family member b9 (BHLHB9), and long intergenic non-protein coding RNA 630 (LINC00630) genes on chromosome X. Transcripts may make use of multiple alternative promoters and polyadenylation signals in this region. Readthrough transcripts may produce proteins identical to the proteins encoded by GPRASP2 or BHLHB9. [provided by RefSeq, Apr 2017]

ARMCX5-GPRASP2 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=-0.85).

BP6

Variant X-102714234-A-G is Benign according to our data. Variant chrX-102714234-A-G is described in ClinVar as [Benign]. Clinvar id is 1226940.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.2 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GPRASP2	NM_001004051.4 linkuse as main transcript	c.-366A>G		5_prime_UTR_variant	4/5	ENST00000483720.7
ARMCX5-GPRASP2	NR_146584.3 linkuse as main transcript	n.763A>G		non_coding_transcript_exon_variant	6/19

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GPRASP2	ENST00000483720.7 linkuse as main transcript	c.-366A>G		5_prime_UTR_variant	4/5	2	NM_001004051.4	P1
ARMCX5-GPRASP2	ENST00000652409.1 linkuse as main transcript	c.-788A>G		5_prime_UTR_variant	4/8			P1

Frequencies

GnomAD3 genomes

AF:

0.114

AC:

12672

AN:

111032

Hom.:

655

Cov.:

AF XY:

0.108

AC XY:

3605

AN XY:

33286

show subpopulations

Gnomad AFR

AF:

0.175

Gnomad AMI

AF:

0.0132

Gnomad AMR

AF:

0.0593

Gnomad ASJ

AF:

0.0709

Gnomad EAS

AF:

0.213

Gnomad SAS

AF:

0.137

Gnomad FIN

AF:

0.133

Gnomad MID

AF:

0.0802

Gnomad NFE

AF:

0.0840

Gnomad OTH

AF:

0.104

GnomAD4 exome

AF:

0.0548

AC:

AN:

310

Hom.:

Cov.:

AF XY:

0.0595

AC XY:

AN XY:

show subpopulations

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.0542

Gnomad4 OTH exome

AF:

0.250

GnomAD4 genome

AF:

0.114

AC:

12680

AN:

111086

Hom.:

657

Cov.:

AF XY:

0.108

AC XY:

3607

AN XY:

33350

show subpopulations

Gnomad4 AFR

AF:

0.175

Gnomad4 AMR

AF:

0.0592

Gnomad4 ASJ

AF:

0.0709

Gnomad4 EAS

AF:

0.213

Gnomad4 SAS

AF:

0.138

Gnomad4 FIN

AF:

0.133

Gnomad4 NFE

AF:

0.0841

Gnomad4 OTH

AF:

0.110

Alfa

AF:

0.107

Hom.:

585

Bravo

AF:

0.112

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	May 12, 2021	- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.85

CADD

Benign

0.60

DANN

Benign

0.72

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