rs9772321
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_047662.2(LOC729732):n.1034+25000A>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 0.235 in 149,712 control chromosomes in the GnomAD database, including 4,883 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 0.24 ( 4883 hom., cov: 31)
Consequence
LOC729732
NR_047662.2 intron, non_coding_transcript
NR_047662.2 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.160
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=-0.99).
BA1
?
GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.265 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC729732 | NR_047662.2 | n.1034+25000A>G | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
ENST00000637678.1 | n.937+25000A>G | intron_variant, non_coding_transcript_variant | 1 | ||||||
ENST00000635775.1 | n.1011+25000A>G | intron_variant, non_coding_transcript_variant | 2 | ||||||
ENST00000636990.1 | n.523-7560A>G | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.235 AC: 35220AN: 149596Hom.: 4876 Cov.: 31
GnomAD3 genomes
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35220
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31
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? AF: 0.235 AC: 35238AN: 149712Hom.: 4883 Cov.: 31 AF XY: 0.231 AC XY: 16881AN XY: 73192
GnomAD4 genome
?
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35238
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149712
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31
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16881
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73192
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Asia WGS
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432
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3472
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