rs41258174

chr22-25563711-T-Cchr22-25563711-T-G

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BS1 BS2

The NR_183563.1(GRK3-AS1):n.605-230A>G variant causes a intron, non coding transcript change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0392 in 152,206 control chromosomes in the GnomAD database, including 133 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 0.039 (133 hom., cov: 32)
• Consequence: GRK3-AS1 NR_183563.1 intron, non_coding_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.0210

Genes affected

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

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.84).
• BS1: Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.0392 (5966/152206) while in subpopulation NFE AF= 0.0427 (2907/68006). AF 95% confidence interval is 0.0414. There are 133 homozygotes in gnomad4. There are 2816 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
• BS2: High Homozygotes in GnomAd at 132 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
GRK3-AS1	NR_183563.1	n.605-230A>G		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
GRK3-AS1	ENST00000668059.1	n.626+379A>G		intron_variant, non_coding_transcript_variant

Frequencies

GnomAD3 genomes AF: 0.0392 AC: 5962 AN: 152088 Hom.: 132 Cov.: 32

Gnomad AFR AF: 0.0378

Gnomad AMI AF: 0.0571

Gnomad AMR AF: 0.0252

Gnomad ASJ AF: 0.0349

Gnomad EAS AF: 0.0131

Gnomad SAS AF: 0.0356

Gnomad FIN AF: 0.0543

Gnomad MID AF: 0.0918

Gnomad NFE AF: 0.0427

Gnomad OTH AF: 0.0430

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0392 AC: 5966 AN: 152206 Hom.: 133 Cov.: 32 AF XY: 0.0378 AC XY: 2816 AN XY: 74408

Gnomad4 AFR AF: 0.0378

Gnomad4 AMR AF: 0.0251

Gnomad4 ASJ AF: 0.0349

Gnomad4 EAS AF: 0.0129

Gnomad4 SAS AF: 0.0361

Gnomad4 FIN AF: 0.0543

Gnomad4 NFE AF: 0.0427

Gnomad4 OTH AF: 0.0426

Alfa AF: 0.0426 Hom.: 15

Bravo AF: 0.0371

Asia WGS AF: 0.0310 AC: 108 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.84
Cadd	Benign	4.7
Dann	Benign	0.64

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs41258174; hg19: chr22-25959678;