rs11090910
Positions:
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_047441696.1(LOC124905135):c.*7201T>C variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.292 in 151,924 control chromosomes in the GnomAD database, including 7,123 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 ( 7119 hom., cov: 32)
Exomes 𝑓: 0.41 ( 4 hom. )
Consequence
LOC124905135
XM_047441696.1 3_prime_UTR
XM_047441696.1 3_prime_UTR
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.508
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 (AFR) allele frequency at 95% confidence interval = 0.39 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
LOC124905135 | XM_047441696.1 | c.*7201T>C | 3_prime_UTR_variant | 2/2 | |||
MIRLET7BHG | NR_027033.2 | n.2579T>C | non_coding_transcript_exon_variant | 6/6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MIRLET7BHG | ENST00000360737.4 | n.2422T>C | non_coding_transcript_exon_variant | 5/5 | 2 |
Frequencies
GnomAD3 genomes ? AF: 0.292 AC: 44315AN: 151760Hom.: 7106 Cov.: 32
GnomAD3 genomes
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32
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GnomAD4 exome AF: 0.413 AC: 19AN: 46Hom.: 4 Cov.: 0 AF XY: 0.444 AC XY: 16AN XY: 36
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GnomAD4 genome ? AF: 0.292 AC: 44360AN: 151878Hom.: 7119 Cov.: 32 AF XY: 0.290 AC XY: 21565AN XY: 74236
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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