chr22-25563342-A-G

Variant names:

• chr22-25563342-A-G
• rs5761122
• ENST00000453811.2:n.532T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000453811.2(GRK3-AS1):​n.532T>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 ENST00000453811.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.49
• Publications: 3 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000453811.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRK3-AS1	NR_183556.1		n.558T>C		non_coding_transcript_exon	Exon 3 of 4
	GRK3-AS1	NR_183557.1		n.561T>C		non_coding_transcript_exon	Exon 3 of 4
	GRK3-AS1	NR_183561.1		n.463T>C		non_coding_transcript_exon	Exon 3 of 4

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRK3-AS1	ENST00000453811.2	TSL:3	n.532T>C		non_coding_transcript_exon	Exon 3 of 4
	GRK3-AS1	ENST00000661676.2		n.813T>C		non_coding_transcript_exon	Exon 2 of 2
	GRK3-AS1	ENST00000666865.2		n.501T>C		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.813 AC: 123642 AN: 152010 Hom.: 51027 Cov.: 31

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: 0 AN: 2 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 2

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AC: 0 AN: 0

European-Finnish (FIN) AC: 0 AN: 0

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.814 AC: 123769 AN: 152128 Hom.: 51097 Cov.: 31 AF XY: 0.819 AC XY: 60899 AN XY: 74360

African (AFR) AF: 0.950 AC: 39419 AN: 41498

American (AMR) AF: 0.825 AC: 12626 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.785 AC: 2725 AN: 3472

East Asian (EAS) AF: 0.943 AC: 4885 AN: 5178

South Asian (SAS) AF: 0.905 AC: 4360 AN: 4818

European-Finnish (FIN) AF: 0.753 AC: 7948 AN: 10556

Middle Eastern (MID) AF: 0.803 AC: 236 AN: 294

European-Non Finnish (NFE) AF: 0.725 AC: 49296 AN: 67990

Other (OTH) AF: 0.781 AC: 1653 AN: 2116

Alfa AF: 0.771 Hom.: 71739

Bravo AF: 0.825

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.98
CADD	Benign	0.013
DANN	Benign	0.24
PhyloP100		-2.5

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs5761122; hg19: chr22-25959309;