chr20-62307707-G-A
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Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_007002.4(ADRM1):c.735G>A(p.Ala245Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00316 in 1,612,068 control chromosomes in the GnomAD database, including 101 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.014 ( 50 hom., cov: 34)
Exomes 𝑓: 0.0020 ( 51 hom. )
Consequence
ADRM1
NM_007002.4 synonymous
NM_007002.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -1.92
Genes affected
ADRM1 (HGNC:15759): (ADRM1 26S proteasome ubiquitin receptor) This gene encodes a member of the adhesion regulating molecule 1 protein family. The encoded protein is a component of the proteasome where it acts as a ubiquitin receptor and recruits the deubiquitinating enzyme, ubiquitin carboxyl-terminal hydrolase L5. Increased levels of the encoded protein are associated with increased cell adhesion, which is likely an indirect effect of this intracellular protein. Dysregulation of this gene has been implicated in carcinogenesis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2013]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -20 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.75).
BP6
Variant 20-62307707-G-A is Benign according to our data. Variant chr20-62307707-G-A is described in ClinVar as [Benign]. Clinvar id is 777606.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.0143 (2178/152312) while in subpopulation AFR AF= 0.0476 (1978/41560). AF 95% confidence interval is 0.0458. There are 50 homozygotes in gnomad4. There are 1013 alleles in male gnomad4 subpopulation. Median coverage is 34. This position pass quality control queck.
BS2
High Homozygotes in GnomAd4 at 50 AR gene
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
ADRM1 | ENST00000253003.7 | c.735G>A | p.Ala245Ala | synonymous_variant | 7/10 | 1 | NM_007002.4 | ENSP00000253003.2 | ||
ADRM1 | ENST00000491935.5 | c.735G>A | p.Ala245Ala | synonymous_variant | 8/11 | 5 | ENSP00000478877.1 | |||
ADRM1 | ENST00000620230.4 | c.618G>A | p.Ala206Ala | synonymous_variant | 6/9 | 5 | ENSP00000480756.1 |
Frequencies
GnomAD3 genomes AF: 0.0143 AC: 2173AN: 152194Hom.: 50 Cov.: 34
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GnomAD3 exomes AF: 0.00456 AC: 1115AN: 244478Hom.: 18 AF XY: 0.00354 AC XY: 471AN XY: 133172
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GnomAD4 exome AF: 0.00200 AC: 2922AN: 1459756Hom.: 51 Cov.: 33 AF XY: 0.00177 AC XY: 1285AN XY: 726194
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GnomAD4 genome AF: 0.0143 AC: 2178AN: 152312Hom.: 50 Cov.: 34 AF XY: 0.0136 AC XY: 1013AN XY: 74480
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | not provided | Breakthrough Genomics, Breakthrough Genomics | - | - - |
Benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | May 08, 2018 | - - |
Computational 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