Variant 11-18934983-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The NM_147199.4(MRGPRX1):c.-199G>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 0.365 in 669,714 control chromosomes in the GnomAD database, including 38,209 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 0.35 ( 8450 hom., cov: 36)

Exomes 𝑓: 0.37 ( 29759 hom. )

Consequence

MRGPRX1
NM_147199.4 5_prime_UTR

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.455

Variant links:

Genes affected

MRGPRX1 (HGNC:17962): (MAS related GPR family member X1) Enables transmembrane signaling receptor activity. Involved in cell surface receptor signaling pathway and response to chloroquine. Predicted to be located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]

MRGPRX1 links:

ENSG00000255244 (HGNC:):

ENSG00000255244 links:

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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=-1.02).

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.4 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
MRGPRX1	NM_001393578.1 link	c.-25-174G>A		intron_variant		ENST00000526914.2	NP_001380507.1
MRGPRX1	NM_147199.4 link	c.-199G>A		5_prime_UTR_variant	1/1		NP_671732.3	Q96LB2W8W3P5

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL	MANE	Protein	UniProt
MRGPRX1	ENST00000526914.2 link	c.-25-174G>A	intron_variant		3	NM_001393578.1	ENSP00000499076.2	Q96LB2A0A494C1K4
MRGPRX1	ENST00000302797.4 link	c.-199G>A	5_prime_UTR_variant	1/1	6		ENSP00000305766.3	Q96LB2
ENSG00000255244	ENST00000528646.1 link	n.-2C>T	upstream_gene_variant		3

Frequencies

GnomAD3 genomes

AF:

0.345

AC:

51358

AN:

148848

Hom.:

8447

Cov.:

show subpopulations

Gnomad AFR

AF:

0.234

Gnomad AMI

AF:

0.260

Gnomad AMR

AF:

0.297

Gnomad ASJ

AF:

0.337

Gnomad EAS

AF:

0.315

Gnomad SAS

AF:

0.415

Gnomad FIN

AF:

0.538

Gnomad MID

AF:

0.347

Gnomad NFE

AF:

0.392

Gnomad OTH

AF:

0.344

GnomAD4 exome

AF:

0.371

AC:

193086

AN:

520748

Hom.:

29759

Cov.:

AF XY:

0.373

AC XY:

99054

AN XY:

265914

show subpopulations

Gnomad4 AFR exome

AF:

0.238

Gnomad4 AMR exome

AF:

0.258

Gnomad4 ASJ exome

AF:

0.332

Gnomad4 EAS exome

AF:

0.307

Gnomad4 SAS exome

AF:

0.377

Gnomad4 FIN exome

AF:

0.521

Gnomad4 NFE exome

AF:

0.371

Gnomad4 OTH exome

AF:

0.366

GnomAD4 genome

AF:

0.345

AC:

51409

AN:

148966

Hom.:

8450

Cov.:

AF XY:

0.352

AC XY:

25578

AN XY:

72696

show subpopulations

Gnomad4 AFR

AF:

0.235

Gnomad4 AMR

AF:

0.297

Gnomad4 ASJ

AF:

0.337

Gnomad4 EAS

AF:

0.315

Gnomad4 SAS

AF:

0.415

Gnomad4 FIN

AF:

0.538

Gnomad4 NFE

AF:

0.393

Gnomad4 OTH

AF:

0.344

Alfa

AF:

0.378

Hom.:

1118

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-1.0

CADD

Benign

1.2

DANN

Benign

0.48

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.020

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

Computational scores

Splicing

Publications

LitVar

Other links and lift over