rs4131535
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XR_007063412.1(LOC124902989):n.7746A>G 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 0.291 in 152,130 control chromosomes in the GnomAD database, including 6,435 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 0.29 ( 6435 hom., cov: 32)
Consequence
LOC124902989
XR_007063412.1 non_coding_transcript_exon
XR_007063412.1 non_coding_transcript_exon
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.21
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=-1.04).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.327 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124902989 | XR_007063412.1 | n.7746A>G | non_coding_transcript_exon_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.291 AC: 44200AN: 152012Hom.: 6432 Cov.: 32
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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: 0.291 AC: 44233AN: 152130Hom.: 6435 Cov.: 32 AF XY: 0.290 AC XY: 21601AN XY: 74374
GnomAD4 genome
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152130
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32
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21601
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74374
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Asia WGS
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1035
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3470
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