rs6119279
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000278980.11(COMMD7):c.84+502T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.578 in 151,836 control chromosomes in the GnomAD database, including 27,763 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 0.58 ( 27763 hom., cov: 30)
Consequence
COMMD7
ENST00000278980.11 intron
ENST00000278980.11 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.484
Genes affected
COMMD7 (HGNC:16223): (COMM domain containing 7) Enables NF-kappaB binding activity. Involved in negative regulation of NF-kappaB transcription factor activity; negative regulation of transcription, DNA-templated; and tumor necrosis factor-mediated signaling pathway. Predicted to be located in cytoplasmic vesicle. Predicted to be integral component of membrane. [provided by Alliance of Genome Resources, Apr 2022]
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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=-0.89).
BA1
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.903 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
COMMD7 | NM_053041.3 | c.84+502T>C | intron_variant | ENST00000278980.11 | NP_444269.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
COMMD7 | ENST00000278980.11 | c.84+502T>C | intron_variant | 1 | NM_053041.3 | ENSP00000278980 | P4 | |||
COMMD7 | ENST00000446419.6 | c.84+502T>C | intron_variant | 2 | ENSP00000395339 | A1 | ||||
COMMD7 | ENST00000474815.2 | c.84+502T>C | intron_variant | 5 | ENSP00000476443 | |||||
COMMD7 | ENST00000610160.1 | c.85-241T>C | intron_variant, NMD_transcript_variant | 2 | ENSP00000476617 |
Frequencies
GnomAD3 genomes AF: 0.578 AC: 87673AN: 151718Hom.: 27716 Cov.: 30
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.578 AC: 87774AN: 151836Hom.: 27763 Cov.: 30 AF XY: 0.583 AC XY: 43215AN XY: 74186
GnomAD4 genome
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2622
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3478
ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
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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