rs7196890
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The 16-56637108-C-A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.352 in 568,024 control chromosomes in the GnomAD database, including 36,226 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 0.34 ( 9038 hom., cov: 33)
Exomes 𝑓: 0.36 ( 27188 hom. )
Consequence
MT1JP
NR_036677.1 downstream_gene
NR_036677.1 downstream_gene
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -3.90
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=-0.95).
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
MT1JP | NR_036677.1 | downstream_gene_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
MT1JP | ENST00000563395.4 | downstream_gene_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.343 AC: 52020AN: 151844Hom.: 9028 Cov.: 33
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GnomAD4 exome AF: 0.355 AC: 147734AN: 416062Hom.: 27188 Cov.: 5 AF XY: 0.361 AC XY: 78565AN XY: 217912
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GnomAD4 genome ? AF: 0.343 AC: 52054AN: 151962Hom.: 9038 Cov.: 33 AF XY: 0.342 AC XY: 25384AN XY: 74232
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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