Variant rs17097921 details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -8 ACMG points: 0P and 8B. BA1

The NM_001197184.3(GPR33):c.418C>T(p.Arg140*) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.994 in 1,536,160 control chromosomes in the GnomAD database, including 759,337 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 0.99 ( 74770 hom., cov: 33)

Exomes 𝑓: 0.99 ( 684567 hom. )

Consequence

GPR33
NM_001197184.3 stop_gained

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 2.16

Variant links:

Genes affected

GPR33 (HGNC:4489): (G protein-coupled receptor 33) This gene has been identified as an orphan chemoattractant G-protein-coupled receptors (GPCR) pseudogene. Studies have shown that the inactivated gene is present as the predominant allele in the human population. A small fraction of the human population has been found to harbor an intact allele.[provided by RefSeq, Oct 2010]

GPR33 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -8 ACMG points.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.992 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR33	NM_001197184.3 linkuse as main transcript	c.418C>T	p.Arg140*	stop_gained	2/2	ENST00000399285.5	NP_001184113.2	Q49SQ1D8VER1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
GPR33	ENST00000399285.5 linkuse as main transcript	c.418C>T	p.Arg140*	stop_gained	2/2	1	NM_001197184.3	ENSP00000421557.1		Q49SQ1

Frequencies

GnomAD3 genomes

AF:

0.991

AC:

150806

AN:

152222

Hom.:

74715

Cov.:

show subpopulations

Gnomad AFR

AF:

0.985

Gnomad AMI

AF:

0.979

Gnomad AMR

AF:

0.994

Gnomad ASJ

AF:

0.996

Gnomad EAS

AF:

0.935

Gnomad SAS

AF:

0.958

Gnomad FIN

AF:

1.00

Gnomad MID

AF:

0.984

Gnomad NFE

AF:

0.999

Gnomad OTH

AF:

0.986

GnomAD4 exome

AF:

0.995

AC:

1376281

AN:

1383820

Hom.:

684567

Cov.:

AF XY:

0.994

AC XY:

678618

AN XY:

682850

show subpopulations

Gnomad4 AFR exome

AF:

0.986

Gnomad4 AMR exome

AF:

0.997

Gnomad4 ASJ exome

AF:

0.995

Gnomad4 EAS exome

AF:

0.935

Gnomad4 SAS exome

AF:

0.967

Gnomad4 FIN exome

AF:

0.999

Gnomad4 NFE exome

AF:

0.999

Gnomad4 OTH exome

AF:

0.989

GnomAD4 genome

AF:

0.991

AC:

150920

AN:

152340

Hom.:

74770

Cov.:

AF XY:

0.991

AC XY:

73790

AN XY:

74488

show subpopulations

Gnomad4 AFR

AF:

0.985

Gnomad4 AMR

AF:

0.994

Gnomad4 ASJ

AF:

0.996

Gnomad4 EAS

AF:

0.935

Gnomad4 SAS

AF:

0.959

Gnomad4 FIN

AF:

1.00

Gnomad4 NFE

AF:

0.999

Gnomad4 OTH

AF:

0.984

Alfa

AF:

0.996

Hom.:

78950

Bravo

AF:

0.990

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.48

CADD

Pathogenic

Vest4

0.34

Splicing

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