rs10461985
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NR_145476.1(GDNF-AS1):n.429+41G>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 0.12 in 151,508 control chromosomes in the GnomAD database, including 1,160 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 ( 1160 hom., cov: 32)
Failed GnomAD Quality Control
Consequence
GDNF-AS1
NR_145476.1 intron, non_coding_transcript
NR_145476.1 intron, non_coding_transcript
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 0.521
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=-0.86).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.18 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
GDNF-AS1 | NR_145476.1 | n.429+41G>A | intron_variant, non_coding_transcript_variant | |||||
GDNF-AS1 | NR_103441.2 | n.410+41G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
GDNF-AS1 | ENST00000503382.6 | n.410+41G>A | intron_variant, non_coding_transcript_variant | 1 | ||||||
GDNF-AS1 | ENST00000510986.2 | n.842+41G>A | intron_variant, non_coding_transcript_variant | 1 | ||||||
GDNF-AS1 | ENST00000514532.3 | n.2719+41G>A | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes AF: 0.120 AC: 18192AN: 151394Hom.: 1158 Cov.: 32
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32
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GnomAD4 exome Data not reliable, filtered out with message: AC0AC: 0AN: 0Hom.: 0 Cov.: 0AC XY: 0AN XY: 0
GnomAD4 exome
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GnomAD4 genome AF: 0.120 AC: 18208AN: 151508Hom.: 1160 Cov.: 32 AF XY: 0.124 AC XY: 9164AN XY: 73986
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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