ENST00000661676.2:n.939T>G

Variant names:

• chr22-25563216-A-C
• rs41258844
• ENST00000661676.2:n.939T>G

Variant summary

Our verdict is Likely benign. The variant received -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000661676.2(GRK3-AS1):​n.939T>G 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 0.000208 in 96,240 control chromosomes in the GnomAD database, with no homozygous occurrence. 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 0.00021 (0 hom., cov: 26)
  • Failed GnomAD Quality Control
• Consequence: GRK3-AS1 ENST00000661676.2 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.17
• Publications: 1 publications found

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000661676.2. 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_183565.1		n.873T>G		non_coding_transcript_exon	Exon 3 of 3
	GRK3-AS1	NR_183566.1		n.589T>G		non_coding_transcript_exon	Exon 3 of 3
	GRK3-AS1	NR_183567.1		n.909T>G		non_coding_transcript_exon	Exon 2 of 2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	GRK3-AS1	ENST00000661676.2		n.939T>G		non_coding_transcript_exon	Exon 2 of 2
	GRK3-AS1	ENST00000666865.2		n.627T>G		non_coding_transcript_exon	Exon 3 of 3
	GRK3-AS1	ENST00000818413.1		n.621T>G		non_coding_transcript_exon	Exon 3 of 3

Frequencies

GnomAD3 genomes AF: 0.000208 AC: 20 AN: 96228 Hom.: 0 Cov.: 26

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000178

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.000587

Gnomad FIN AF: 0.000137

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000262

Gnomad OTH AF: 0.000760

GnomAD4 exome Data not reliable, filtered out with message: AC0;AS_VQSR AC: 0 AN: 0 Hom.: 0 Cov.: 0 AC XY: 0 AN XY: 0

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) AC: 0 AN: 0

Other (OTH) AC: 0 AN: 0

GnomAD4 genome AF: 0.000208 AC: 20 AN: 96240 Hom.: 0 Cov.: 26 AF XY: 0.000213 AC XY: 10 AN XY: 46892

African (AFR) AF: 0.00 AC: 0 AN: 11312

American (AMR) AF: 0.000177 AC: 2 AN: 11286

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 2604

East Asian (EAS) AF: 0.00 AC: 0 AN: 4564

South Asian (SAS) AF: 0.000588 AC: 2 AN: 3404

European-Finnish (FIN) AF: 0.000137 AC: 1 AN: 7300

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 190

European-Non Finnish (NFE) AF: 0.000262 AC: 14 AN: 53514

Other (OTH) AF: 0.000751 AC: 1 AN: 1332

Alfa AF: 0.0346 Hom.: 3

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.3
DANN	Benign	0.83
PhyloP100		1.2

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs41258844;

hg19: chr22-25959183;