rs28385141
Variant summary
Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBS1BS2
The NM_000057.4(BLM):c.3613G>A(p.Val1205Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000388 in 1,614,150 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. 13/21 in silico tools predict 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. V1205A) has been classified as Uncertain significance.
Frequency
Consequence
NM_000057.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
BLM | NM_000057.4 | c.3613G>A | p.Val1205Ile | missense_variant | 19/22 | ENST00000355112.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
BLM | ENST00000355112.8 | c.3613G>A | p.Val1205Ile | missense_variant | 19/22 | 1 | NM_000057.4 | P2 |
Frequencies
GnomAD3 genomes AF: 0.00227 AC: 345AN: 152198Hom.: 2 Cov.: 32
GnomAD3 exomes AF: 0.000593 AC: 149AN: 251308Hom.: 0 AF XY: 0.000493 AC XY: 67AN XY: 135828
GnomAD4 exome AF: 0.000192 AC: 280AN: 1461834Hom.: 0 Cov.: 32 AF XY: 0.000161 AC XY: 117AN XY: 727220
GnomAD4 genome AF: 0.00227 AC: 346AN: 152316Hom.: 2 Cov.: 32 AF XY: 0.00207 AC XY: 154AN XY: 74482
ClinVar
Submissions by phenotype
Bloom syndrome Benign:5
Likely benign, criteria provided, single submitter | clinical testing | Mendelics | May 28, 2019 | - - |
Likely benign, criteria provided, single submitter | clinical testing | ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories | Oct 13, 2023 | - - |
Benign, no assertion criteria provided | clinical testing | Natera, Inc. | Jun 01, 2020 | - - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Feb 01, 2024 | - - |
Likely benign, criteria provided, single submitter | clinical testing | KCCC/NGS Laboratory, Kuwait Cancer Control Center | Jul 07, 2023 | - - |
not specified Benign:2Other:1
Benign, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Mar 05, 2021 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | Jul 13, 2018 | Variant summary: BLM c.3613G>A (p.Val1205Ile) results in a conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 0.00078 in 278434 control chromosomes in the gnomAD database and publications, including 1 homozygote. The observed variant frequency within African control individuals in the gnomAD database is approximately 2.3-fold of the estimated maximal expected allele frequency for a pathogenic variant in BLM causing Bloom Syndrome phenotype (0.0035), strongly suggesting that the variant is a benign polymorphism found primarily in populations of African origin. The variant, c.3613G>A, has not been reported in the literature in individuals affected with Bloom Syndrome and was reported in healthy controls (Bodian_2014). To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Two clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation and classified the variant as benign/likely benign. Based on the evidence outlined above, the variant was classified as likely benign. - |
not provided, no classification provided | reference population | ITMI | Sep 19, 2013 | - - |
Hereditary cancer-predisposing syndrome Benign:2
Benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Jul 02, 2018 | This alteration is classified as benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
Benign, criteria provided, single submitter | curation | Sema4, Sema4 | Apr 01, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at