rs9807334
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_007066371.1(LOC107985152):n.1408C>T 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 0.0644 in 152,250 control chromosomes in the GnomAD database, including 499 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 0.064 ( 499 hom., cov: 32)
Consequence
LOC107985152
XR_007066371.1 non_coding_transcript_exon
XR_007066371.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: 1.09
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=-0.91).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.103 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC107985152 | XR_007066371.1 | n.1408C>T | non_coding_transcript_exon_variant | 1/3 | |||
LOC107985152 | XR_001753449.3 | n.1002C>T | non_coding_transcript_exon_variant | 1/3 | |||
LOC107985152 | XR_002958225.2 | n.1408C>T | non_coding_transcript_exon_variant | 1/4 | |||
LOC107985152 | XR_007066370.1 | n.178-13451C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|
Frequencies
GnomAD3 genomes ? AF: 0.0644 AC: 9802AN: 152132Hom.: 499 Cov.: 32
GnomAD3 genomes
?
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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: 0.0644 AC: 9804AN: 152250Hom.: 499 Cov.: 32 AF XY: 0.0611 AC XY: 4552AN XY: 74440
GnomAD4 genome
?
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AC:
9804
AN:
152250
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32
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AC XY:
4552
AN XY:
74440
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32
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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
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at