rs8070085
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The ENST00000590996.6(NBR1):c.695+165A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.345 in 636,402 control chromosomes in the GnomAD database, including 39,248 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 0.32 ( 8044 hom., cov: 32)
Exomes 𝑓: 0.35 ( 31204 hom. )
Consequence
NBR1
ENST00000590996.6 intron
ENST00000590996.6 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.0300
Genes affected
NBR1 (HGNC:6746): (NBR1 autophagy cargo receptor) The protein encoded by this gene was originally identified as an ovarian tumor antigen monitored in ovarian cancer. The encoded protein contains a B-box/coiled-coil motif, which is present in many genes with transformation potential. It functions as a specific autophagy receptor for the selective autophagic degradation of peroxisomes by forming intracellular inclusions with ubiquitylated autophagic substrates. This gene is located on a region of chromosome 17q21.1 that is in close proximity to the BRCA1 tumor suppressor gene. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Apr 2014]
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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=-0.9).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.478 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NBR1 | NM_005899.5 | c.695+165A>G | intron_variant | ENST00000590996.6 | NP_005890.2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NBR1 | ENST00000590996.6 | c.695+165A>G | intron_variant | 1 | NM_005899.5 | ENSP00000466667 | P1 |
Frequencies
GnomAD3 genomes AF: 0.318 AC: 48315AN: 151970Hom.: 8038 Cov.: 32
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GnomAD4 exome AF: 0.354 AC: 171492AN: 484314Hom.: 31204 Cov.: 6 AF XY: 0.362 AC XY: 92715AN XY: 255834
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GnomAD4 genome AF: 0.318 AC: 48351AN: 152088Hom.: 8044 Cov.: 32 AF XY: 0.324 AC XY: 24104AN XY: 74360
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ClinVar
Not reported inComputational scores
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at