rs11001553
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_038277.1(PRKG1-AS1):n.583+257G>A 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 0.121 in 152,120 control chromosomes in the GnomAD database, including 1,303 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 0.12 ( 1303 hom., cov: 32)
Consequence
PRKG1-AS1
NR_038277.1 intron, non_coding_transcript
NR_038277.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.33
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=-0.87).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PRKG1-AS1 | NR_038277.1 | n.583+257G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PRKG1-AS1 | ENST00000452247.7 | n.130+257G>A | intron_variant, non_coding_transcript_variant | 5 | |||||
PRKG1-AS1 | ENST00000420193.1 | n.583+257G>A | intron_variant, non_coding_transcript_variant | 3 | |||||
PRKG1-AS1 | ENST00000649494.1 | n.962+257G>A | intron_variant, non_coding_transcript_variant | ||||||
PRKG1-AS1 | ENST00000658196.1 | n.81+257G>A | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes ? AF: 0.121 AC: 18401AN: 152002Hom.: 1298 Cov.: 32
GnomAD3 genomes
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18401
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152002
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32
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.121 AC: 18433AN: 152120Hom.: 1303 Cov.: 32 AF XY: 0.120 AC XY: 8920AN XY: 74360
GnomAD4 genome
?
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18433
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152120
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32
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8920
AN XY:
74360
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Asia WGS
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739
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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