rs141865425
Variant summary
Our verdict is Benign. Variant got -16 ACMG points: 0P and 16B. BP4_StrongBP6_Very_StrongBS2
The ENST00000259089.9(BLK):c.713G>A(p.Arg238Gln) variant causes a missense change. The variant allele was found at a frequency of 0.00456 in 1,614,156 control chromosomes in the GnomAD database, including 24 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R238W) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000259089.9 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -16 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
BLK | NM_001715.3 | c.713G>A | p.Arg238Gln | missense_variant | 8/13 | ENST00000259089.9 | NP_001706.2 | |
LOC105379241 | XR_948956.3 | n.1117+293C>T | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
BLK | ENST00000259089.9 | c.713G>A | p.Arg238Gln | missense_variant | 8/13 | 1 | NM_001715.3 | ENSP00000259089 | P1 | |
ENST00000602626.2 | n.622+293C>T | intron_variant, non_coding_transcript_variant |
Frequencies
GnomAD3 genomes AF: 0.00299 AC: 455AN: 152158Hom.: 1 Cov.: 32
GnomAD3 exomes AF: 0.00307 AC: 773AN: 251430Hom.: 4 AF XY: 0.00328 AC XY: 446AN XY: 135894
GnomAD4 exome AF: 0.00473 AC: 6909AN: 1461880Hom.: 23 Cov.: 31 AF XY: 0.00466 AC XY: 3391AN XY: 727240
GnomAD4 genome AF: 0.00299 AC: 455AN: 152276Hom.: 1 Cov.: 32 AF XY: 0.00317 AC XY: 236AN XY: 74468
ClinVar
Submissions by phenotype
not provided Benign:5
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Oct 19, 2020 | This variant is associated with the following publications: (PMID: 31101814, 28766502) - |
Likely benign, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 15, 2024 | - - |
Likely benign, no assertion criteria provided | clinical testing | Clinical Genetics DNA and cytogenetics Diagnostics Lab, Erasmus MC, Erasmus Medical Center | - | - - |
Likely benign, no assertion criteria provided | clinical testing | Genome Diagnostics Laboratory, University Medical Center Utrecht | - | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Apr 01, 2024 | ENSG00000269954: BS2 - |
not specified Benign:2
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | May 24, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
Maturity-onset diabetes of the young type 11 Benign:2
Benign, criteria provided, single submitter | clinical testing | Illumina Laboratory Services, Illumina | Jan 12, 2018 | 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 benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease. - |
Benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Sep 10, 2023 | - - |
Systemic lupus erythematosus Pathogenic:1
Pathogenic, no assertion criteria provided | research | Carola Vinuesa Lab, John Curtin School of Medical Research | - | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at