Genetic Variant GRK3-AS1:n.310T>C (chr22-25563342-A-G) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000453811.1(GRK3-AS1):n.310T>C variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.814 in 152,128 control chromosomes in the GnomAD database, including 51,097 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 0.81 ( 51097 hom., cov: 31)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

GRK3-AS1
ENST00000453811.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.49

Variant links:

Genes affected

GRK3-AS1 (HGNC:55679): (GRK3 antisense RNA 1)

GRK3-AS1 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=-0.98).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.942 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
GRK3-AS1	NR_183556.1 link	n.558T>C	non_coding_transcript_exon_variant	Exon 3 of 4
GRK3-AS1	NR_183557.1 link	n.561T>C	non_coding_transcript_exon_variant	Exon 3 of 4
GRK3-AS1	NR_183561.1 link	n.463T>C	non_coding_transcript_exon_variant	Exon 3 of 4

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
GRK3-AS1	ENST00000453811.1 link	n.310T>C	non_coding_transcript_exon_variant	Exon 2 of 3	3
GRK3-AS1	ENST00000661676.1 link	n.770T>C	non_coding_transcript_exon_variant	Exon 2 of 2
GRK3-AS1	ENST00000666865.1 link	n.232T>C	non_coding_transcript_exon_variant	Exon 2 of 2

Frequencies

GnomAD3 genomes

AF:

0.813

AC:

123642

AN:

152010

Hom.:

51027

Cov.:

show subpopulations

Gnomad AFR

AF:

0.950

Gnomad AMI

AF:

0.682

Gnomad AMR

AF:

0.825

Gnomad ASJ

AF:

0.785

Gnomad EAS

AF:

0.944

Gnomad SAS

AF:

0.906

Gnomad FIN

AF:

0.753

Gnomad MID

AF:

0.797

Gnomad NFE

AF:

0.725

Gnomad OTH

AF:

0.780

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

Gnomad4 NFE exome

AF:

0.00

GnomAD4 genome

AF:

0.814

AC:

123769

AN:

152128

Hom.:

51097

Cov.:

AF XY:

0.819

AC XY:

60899

AN XY:

74360

show subpopulations

Gnomad4 AFR

AF:

0.950

Gnomad4 AMR

AF:

0.825

Gnomad4 ASJ

AF:

0.785

Gnomad4 EAS

AF:

0.943

Gnomad4 SAS

AF:

0.905

Gnomad4 FIN

AF:

0.753

Gnomad4 NFE

AF:

0.725

Gnomad4 OTH

AF:

0.781

Alfa

AF:

0.734

Hom.:

5672

Bravo

AF:

0.825

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.98

CADD

Benign

0.013

DANN

Benign

0.24

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