10-16824206-C-T
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBS1BS2
The NM_001081.4(CUBN):c.*769G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00309 in 152,224 control chromosomes in the GnomAD database, including 3 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
Consequence
NM_001081.4 3_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- Imerslund-Grasbeck syndrome type 1Inheritance: AR Classification: DEFINITIVE, STRONG Submitted by: Labcorp Genetics (formerly Invitae), Ambry Genetics, Laboratory for Molecular Medicine
- proteinuria, chronic benignInheritance: AR Classification: STRONG Submitted by: Labcorp Genetics (formerly Invitae)
- Imerslund-Grasbeck syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Our verdict: Benign. The variant received -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CUBN | NM_001081.4 | c.*769G>A | 3_prime_UTR_variant | Exon 67 of 67 | ENST00000377833.10 | NP_001072.2 | ||
CUBN | XM_011519709.3 | c.*769G>A | 3_prime_UTR_variant | Exon 41 of 41 | XP_011518011.1 | |||
CUBN | XM_011519710.3 | c.*769G>A | 3_prime_UTR_variant | Exon 41 of 41 | XP_011518012.1 | |||
CUBN | XM_011519711.4 | c.*769G>A | 3_prime_UTR_variant | Exon 40 of 40 | XP_011518013.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00310 AC: 472AN: 152106Hom.: 3 Cov.: 32 show subpopulations
GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0AN: 160Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0AN XY: 90
GnomAD4 genome AF: 0.00309 AC: 471AN: 152224Hom.: 3 Cov.: 32 AF XY: 0.00280 AC XY: 208AN XY: 74408 show subpopulations
ClinVar
Submissions by phenotype
Imerslund-Grasbeck syndrome type 1 Benign:1
This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as likely benign is not then subjected to further curation. The score for this variant resulted in a classification of likely benign for this disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at