Variant 22-25564140-A-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The ENST00000422876.1(GRK3-AS1):n.11T>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)

Consequence

GRK3-AS1
ENST00000422876.1 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.48

Variant links:

Genes affected

GRK3-AS1 (HGNC:):

GRK3-AS1 links:

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ACMG classification

Classification made for transcript

Verdict is Likely_benign. Variant got -2 ACMG points.

PM2

Very rare variant in population databases, with high coverage;

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.84).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
GRK3-AS1	NR_183556.1 linkuse as main transcript	n.368T>A	non_coding_transcript_exon_variant	2/4
GRK3-AS1	NR_183557.1 linkuse as main transcript	n.371T>A	non_coding_transcript_exon_variant	2/4
GRK3-AS1	NR_183558.1 linkuse as main transcript	n.371T>A	non_coding_transcript_exon_variant	2/3

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
GRK3-AS1	ENST00000422876.1 linkuse as main transcript	n.11T>A	non_coding_transcript_exon_variant	1/2	2
GRK3-AS1	ENST00000453811.1 linkuse as main transcript	n.120T>A	non_coding_transcript_exon_variant	1/3	3
GRK3-AS1	ENST00000661676.1 linkuse as main transcript	n.580T>A	non_coding_transcript_exon_variant	1/2

Frequencies

GnomAD3 genomes

Cov.:

GnomAD4 exome

Cov.:

GnomAD4 genome

Cov.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.80

DANN

Benign

0.65

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