rs130058
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_047419660.1(LOC105377864):c.-3742-10962T>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.268 in 673,436 control chromosomes in the GnomAD database, including 26,820 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 0.23 ( 5071 hom., cov: 32)
Exomes 𝑓: 0.28 ( 21749 hom. )
Consequence
LOC105377864
XM_047419660.1 intron
XM_047419660.1 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.677
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=-0.54).
BA1
?
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.295 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC105377864 | XM_047419660.1 | c.-3742-10962T>A | intron_variant | ||||
LOC105377864 | XM_047419659.1 | c.-10895T>A | 5_prime_UTR_variant | 2/6 | |||
LOC105377864 | XM_047419661.1 | c.-3917+446T>A | intron_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
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Frequencies
GnomAD3 genomes ? AF: 0.232 AC: 35268AN: 151876Hom.: 5069 Cov.: 32
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GnomAD4 exome AF: 0.278 AC: 145206AN: 521440Hom.: 21749 Cov.: 6 AF XY: 0.278 AC XY: 75293AN XY: 271252
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GnomAD4 genome ? AF: 0.232 AC: 35280AN: 151996Hom.: 5071 Cov.: 32 AF XY: 0.235 AC XY: 17495AN XY: 74296
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3478
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at