rs41258274
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NR_183563.1(GRK3-AS1):n.742G>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 0.0194 in 152,262 control chromosomes in the GnomAD database, including 44 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 0.019 ( 44 hom., cov: 31)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control
Consequence
GRK3-AS1
NR_183563.1 non_coding_transcript_exon
NR_183563.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.368
Genes affected
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -12 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.82).
BS1
?
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0194 (2949/152262) while in subpopulation AFR AF= 0.0326 (1354/41524). AF 95% confidence interval is 0.0312. There are 44 homozygotes in gnomad4. There are 1394 alleles in male gnomad4 subpopulation. This position pass quality control queck.
BS2
?
High Homozygotes in GnomAd at 43 gene
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
GRK3-AS1 | NR_183563.1 | n.742G>C | non_coding_transcript_exon_variant | 3/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
GRK3-AS1 | ENST00000668059.1 | n.626+746G>C | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.0193 AC: 2942AN: 152144Hom.: 43 Cov.: 31
GnomAD3 genomes
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31
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GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 8Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 8
GnomAD4 exome
Data not reliable, filtered out with message: AC0
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GnomAD4 genome ? AF: 0.0194 AC: 2949AN: 152262Hom.: 44 Cov.: 31 AF XY: 0.0187 AC XY: 1394AN XY: 74464
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?
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2949
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31
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59
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at