Variant rs3759216 details in Genebe, Genetics Data Aggregator

Variant summary

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

The XM_011520623.4(GPR19):c.-205+559C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.386 in 152,116 control chromosomes in the GnomAD database, including 12,103 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 0.39 ( 12103 hom., cov: 32)

Exomes 𝑓: 0.50 ( 0 hom. )

Consequence

GPR19
XM_011520623.4 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.840

Variant links:

Genes affected

GPR19 (HGNC:4473): (G protein-coupled receptor 19) Predicted to enable G protein-coupled receptor activity. Predicted to be involved in G protein-coupled receptor signaling pathway. Located in cilium. [provided by Alliance of Genome Resources, Apr 2022]

GPR19 links:

CDKN1B (HGNC:):

CDKN1B links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.68).

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.446 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
GPR19	XM_011520623.4 linkuse as main transcript	c.-205+559C>T		intron_variant			XP_011518925.1

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
CDKN1B	ENST00000682080.1 linkuse as main transcript	n.2305G>A	non_coding_transcript_exon_variant	3/3
CDKN1B	ENST00000477087.1 linkuse as main transcript	n.47+48G>A	intron_variant		3
CDKN1B	ENST00000682620.1 linkuse as main transcript	n.1631-3673G>A	intron_variant
CDKN1B	ENST00000684771.1 linkuse as main transcript	n.585-3673G>A	intron_variant

Frequencies

GnomAD3 genomes

AF:

0.387

AC:

58777

AN:

151992

Hom.:

12104

Cov.:

show subpopulations

Gnomad AFR

AF:

0.235

Gnomad AMI

AF:

0.361

Gnomad AMR

AF:

0.381

Gnomad ASJ

AF:

0.472

Gnomad EAS

AF:

0.438

Gnomad SAS

AF:

0.448

Gnomad FIN

AF:

0.505

Gnomad MID

AF:

0.345

Gnomad NFE

AF:

0.450

Gnomad OTH

AF:

0.377

GnomAD4 exome

AF:

0.500

AC:

AN:

Hom.:

Cov.:

AF XY:

0.500

AC XY:

AN XY:

show subpopulations

Gnomad4 FIN exome

AF:

0.500

Gnomad4 NFE exome

AF:

0.500

Gnomad4 OTH exome

AF:

0.500

GnomAD4 genome

AF:

0.386

AC:

58783

AN:

152110

Hom.:

12103

Cov.:

AF XY:

0.390

AC XY:

29025

AN XY:

74382

show subpopulations

Gnomad4 AFR

AF:

0.235

Gnomad4 AMR

AF:

0.381

Gnomad4 ASJ

AF:

0.472

Gnomad4 EAS

AF:

0.438

Gnomad4 SAS

AF:

0.449

Gnomad4 FIN

AF:

0.505

Gnomad4 NFE

AF:

0.450

Gnomad4 OTH

AF:

0.375

Alfa

AF:

0.439

Hom.:

8677

Bravo

AF:

0.373

Asia WGS

AF:

0.403

AC:

1400

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.68

CADD

Benign

DANN

Benign

0.80

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