rs10520842
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_109946.1(RETREG1-AS1):n.1158+852G>T 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 0.0797 in 152,108 control chromosomes in the GnomAD database, including 648 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 0.080 ( 648 hom., cov: 32)
Consequence
RETREG1-AS1
NR_109946.1 intron, non_coding_transcript
NR_109946.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.395
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=-0.84).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.199 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RETREG1-AS1 | NR_109946.1 | n.1158+852G>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RETREG1-AS1 | ENST00000653650.1 | n.329+10122G>T | intron_variant, non_coding_transcript_variant | ||||||
RETREG1-AS1 | ENST00000700847.1 | n.905G>T | non_coding_transcript_exon_variant | 2/2 | |||||
RETREG1-AS1 | ENST00000499131.1 | n.1158+852G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.0797 AC: 12118AN: 151990Hom.: 647 Cov.: 32
GnomAD3 genomes
?
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151990
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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: 0.0797 AC: 12116AN: 152108Hom.: 648 Cov.: 32 AF XY: 0.0824 AC XY: 6123AN XY: 74338
GnomAD4 genome
?
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12116
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152108
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32
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6123
AN XY:
74338
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566
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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