rs146504061

chr15-90754819-A-G

Variant summary

Our verdict is Likely benign. Variant got -1 ACMG points: 2P and 3B. PM2 BP4_Moderate BP6

The NM_000057.4(BLM):c.968A>G(p.Lys323Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000893 in 1,613,702 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 12/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. K323Q) has been classified as Uncertain significance.

• Frequency:
  • Genomes: 𝑓 0.00052 (0 hom., cov: 32)
  • Exomes 𝑓: 0.00093 (0 hom.)
• Consequence: BLM NM_000057.4 missense
• Clinical Significance: Conflicting classifications of pathogenicity criteria provided, conflicting classifications U:12 B:2 O:1
• Conservation: PhyloP100: 3.11

Genes affected

BLM (HGNC:1058): (BLM RecQ like helicase) The Bloom syndrome is an autosomal recessive disorder characterized by growth deficiency, microcephaly and immunodeficiency among others. It is caused by homozygous or compound heterozygous mutation in the gene encoding DNA helicase RecQ protein on chromosome 15q26. This Bloom-associated helicase unwinds a variety of DNA substrates including Holliday junction, and is involved in several pathways contributing to the maintenance of genome stability. Identification of pathogenic Bloom variants is required for heterozygote testing in at-risk families. [provided by RefSeq, May 2020]

ACMG classification

Verdict is Likely_benign. Variant got -1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.11627719).
• BP6: Variant 15-90754819-A-G is Benign according to our data. Variant chr15-90754819-A-G is described in ClinVar as [Conflicting_classifications_of_pathogenicity]. Clinvar id is 127518.We mark this variant Likely_benign, oryginal submissions are: {not_provided=1, Uncertain_significance=10, Likely_benign=2}.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
BLM	NM_000057.4	c.968A>G	p.Lys323Arg	missense_variant	5/22	ENST00000355112.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
BLM	ENST00000355112.8	c.968A>G	p.Lys323Arg	missense_variant	5/22	1	NM_000057.4	P2

Frequencies

GnomAD3 genomes AF: 0.000519 AC: 79 AN: 152200 Hom.: 0 Cov.: 32

Gnomad AFR AF: 0.000193

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.000131

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.000999

Gnomad OTH AF: 0.000478

GnomAD3 exomes AF: 0.000371 AC: 93 AN: 250780 Hom.: 0 AF XY: 0.000369 AC XY: 50 AN XY: 135548

Gnomad AFR exome AF: 0.000185

Gnomad AMR exome AF: 0.000116

Gnomad ASJ exome AF: 0.00

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.000732

Gnomad OTH exome AF: 0.000491

GnomAD4 exome AF: 0.000932 AC: 1362 AN: 1461502 Hom.: 0 Cov.: 31 AF XY: 0.000923 AC XY: 671 AN XY: 727024

Gnomad4 AFR exome AF: 0.000239

Gnomad4 AMR exome AF: 0.000112

Gnomad4 ASJ exome AF: 0.00

Gnomad4 EAS exome AF: 0.00

Gnomad4 SAS exome AF: 0.0000116

Gnomad4 FIN exome AF: 0.0000188

Gnomad4 NFE exome AF: 0.00116

Gnomad4 OTH exome AF: 0.000894

GnomAD4 genome AF: 0.000519 AC: 79 AN: 152200 Hom.: 0 Cov.: 32 AF XY: 0.000498 AC XY: 37 AN XY: 74356

Gnomad4 AFR AF: 0.000193

Gnomad4 AMR AF: 0.000131

Gnomad4 ASJ AF: 0.00

Gnomad4 EAS AF: 0.00

Gnomad4 SAS AF: 0.00

Gnomad4 FIN AF: 0.00

Gnomad4 NFE AF: 0.000999

Gnomad4 OTH AF: 0.000478

Alfa AF: 0.000859 Hom.: 0

Bravo AF: 0.000427

TwinsUK AF: 0.00108 AC: 4

ALSPAC AF: 0.00130 AC: 5

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000698 AC: 6

ExAC AF: 0.000288 AC: 35

EpiCase AF: 0.000763

EpiControl AF: 0.000712

ClinVar

Significance: Conflicting classifications of pathogenicity

Submissions summary: Uncertain:12 Benign:2 Other:1

Revision: criteria provided, conflicting classifications

Submissions by phenotype

Bloom syndrome Uncertain:5

Uncertain significance, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Apr 02, 2022	- -
Uncertain significance, criteria provided, single submitter	clinical testing	St. Jude Molecular Pathology, St. Jude Children's Research Hospital	Jul 11, 2023	The BLM c.968A>G (p.Lys323Arg) missense change has a maximum subpopulation frequency of 0.07% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org). The in silico tool REVEL predicts a benign effect on protein function, but to our knowledge this prediction has not been confirmed by functional studies. To our knowledge, this variant has not been reported in individuals with Bloom syndrome. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Invitae	Feb 01, 2024	This sequence change replaces lysine, which is basic and polar, with arginine, which is basic and polar, at codon 323 of the BLM protein (p.Lys323Arg). This variant is present in population databases (rs146504061, gnomAD 0.07%). This missense change has been observed in individual(s) with breast cancer (PMID: 23028338). ClinVar contains an entry for this variant (Variation ID: 127518). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt BLM protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. -
Uncertain significance, no assertion criteria provided	clinical testing	Natera, Inc.	Oct 17, 2017	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Apr 28, 2017	This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). Publications were found based on this search. However, the evidence from the literature, in combination with allele frequency data from public databases where available, was not sufficient to rule this variant in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance. -

not provided Uncertain:4

Uncertain significance, criteria provided, single submitter	clinical testing	GeneDx	Oct 03, 2023	In silico analysis supports that this missense variant does not alter protein structure/function; Observed in an individual with high grade serous ovarian carcinoma with a family history suggestive of Lynch syndrome, who also harbored pathogenic variants in BRCA1 and RAD51C (Infante et al., 2022); Observed in individuals with personal or family history including breast cancer, renal cell carcinoma, neuroblastoma, mesothelioma, and Lynch syndrome-related cancers (Dalgliesh et al., 2010; Thompson et al., 2012; Zhang et al., 2015; Martin-Morales et al., 2018; Bononi et al., 2020; Guindalini et al., 2022); This variant is associated with the following publications: (PMID: 24728327, 23028338, 22829774, 28873162, 28944238, 20054297, 30256826, 26580448, 30171174, 33318203, 35264596, 33436027, 36232793, 35892882, 34117267, 33606809) -
Uncertain significance, no assertion criteria provided	clinical testing	Department of Pathology and Laboratory Medicine, Sinai Health System	-	The BLM p.Lys323Arg variant was identified in dbSNP (ID: rs146504061), ClinVar (classified as VUS by Invitae, Ambry Genetics, Mendelics, Fulgent Genetics and GeneDx for Bloom syndrome and Hereditary cancer-predisposing syndrome) and LOVD 3.0 (classified as a VUS) but was not identified in Cosmic. The variant was also found in control databases in 109 of 282184 chromosomes at a frequency of 0.000386 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: European (non-Finnish) in 96 of 128798 chromosomes (freq: 0.000745), Other in 3 of 7198 chromosomes (freq: 0.000417), African in 6 of 24952 chromosomes (freq: 0.000241) and Latino in 4 of 35350 chromosomes (freq: 0.000113), while the variant was not observed in the Ashkenazi Jewish, East Asian, European (Finnish) and South Asian populations. This variant was identified in 1/681 healthy individuals in a study assessing variation in cancer genes in a healthy population (Bodian_2014_PMID 24728327). Another study identified the K323R variant in 1/453 cases of breast cancer (Thompson_2012_PMID 23028338). The variant occurs outside of the splicing consensus sequence and in silico or computational prediction software programs (SpliceSiteFinder, MaxEntScan, NNSPLICE, GeneSplicer) do not predict a difference in splicing. The p.Lys323 residue is not conserved in mammals and computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) provide inconsistent predictions regarding the impact to the protein; this information is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance. -
Uncertain significance, criteria provided, single submitter	clinical testing	Quest Diagnostics Nichols Institute San Juan Capistrano	Jul 31, 2023	In the published literature, the variant has been reported in individuals with Li-Fraumeni syndrome (PMID: 22829774 (2012)), breast cancer (PMID: 35264596 (2022), 23028338 (2012)), colon polyps (PMID: 33436027 (2021)), mesothelioma and/or melanoma (PMID: 33318203 (2020)), and neuroblastoma (PMID: 26580448 (2015)). The frequency of this variant in the general population, 0.0012 (61/50710 chromosomes in North-Western European subpopulation (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is higher than would generally be expected for pathogenic variants in this gene. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded conflicting predictions that this variant is benign or damaging. Based on the available information, we are unable to determine the clinical significance of this variant. -
Uncertain significance, criteria provided, single submitter	clinical testing	Institute for Clinical Genetics, University Hospital TU Dresden, University Hospital TU Dresden	Nov 03, 2021	- -

not specified Uncertain:2 Other:1

not provided, no classification provided	reference population	ITMI	Sep 19, 2013	- -
Uncertain significance, criteria provided, single submitter	clinical testing	Genetic Services Laboratory, University of Chicago	Nov 29, 2021	DNA sequence analysis of the BLM gene demonstrated a sequence change, c.968A>G, in exon 5 that results in an amino acid change, p.Lys323Arg. This sequence change has been previously described in a family with breast cancer (PMID: 23028338). This sequence change has been described in the gnomAD database with a low population frequency of 0.075% in non-Finnish Europeans (dbSNP rs146504061). The p.Lys323Arg change affects a moderately conserved amino acid residue located in a domain of the BLM protein that is not known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Lys323Arg substitution. Due to these contrasting evidences and the lack of functional studies, the clinical significance of the p.Lys323Arg change remains unknown at this time. -
Uncertain significance, criteria provided, single submitter	clinical testing	Women's Health and Genetics/Laboratory Corporation of America, LabCorp	Jun 29, 2023	Variant summary: BLM c.968A>G (p.Lys323Arg) results in a conservative amino acid change located in the RecQ-like DNA helicase BLM, N-terminal domain (IPR032437) of 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 0.00037 in 252142 control chromosomes (gnomAD). This frequency is not significantly higher than estimated for a pathogenic variant in BLM causing Bloom Syndrome (0.00037 vs 0.0035), allowing no conclusion about variant significance. c.968A>G has been reported in the literature in individuals affected with various cancers without strong evidence of causality, as well as in unaffected controls (e.g. Bodian_2014, Bononi_2020, Guindalini_2022, Infante_2022, Li_2021, Mondschein_82022, Patel_2021, Paulo_2018, Sandoval_2021, Zhang_2015, Martin-Morales_2018). These reports do not provide unequivocal conclusions about association of the variant with Bloom Syndrome. Co-occurrence with other pathogenic variants has been reported in an ovarian cancer patient (BRCA1 c.4165_4166del, p.Gln1388_Ser1389insTer; RAD51C c.709C>T, p.Arg237Ter; Infante_2022), providing supporting evidence for a benign role. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. The following publications have been ascertained in the context of this evaluation (PMID: 33436027, 36232793, 26580448, 35264596, 24728327, 29659569, 35892882, 34117267, 33318203, 33606809, 30256826). 11 submitters have cited clinical-significance assessments for this variant to ClinVar after 2014, and classified it as uncertain significance (n=10) or likely benign (n=1). Based on the evidence outlined above, the variant was classified as uncertain significance. -

Hereditary cancer-predisposing syndrome Uncertain:1 Benign:1

Uncertain significance, criteria provided, single submitter	curation	Sema4, Sema4	Jan 04, 2022	- -
Likely benign, criteria provided, single submitter	clinical testing	Ambry Genetics	Jun 28, 2022	This alteration is classified as likely 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. -

Hereditary cancer Benign:1

Likely benign, criteria provided, single submitter

clinical testing

Mendelics

Jan 23, 2024

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.081
BayesDel_addAF	Benign	-0.37	T
BayesDel_noAF	Benign	-0.34
Cadd	Benign	18
Dann	Uncertain	1.0
DEOGEN2	Benign	0.10	T;.
Eigen	Uncertain	0.41
Eigen_PC	Uncertain	0.40
FATHMM_MKL	Uncertain	0.94	D
LIST_S2	Benign	0.60	T;T
M_CAP	Benign	0.071	D
MetaRNN	Benign	0.12	T;T
MetaSVM	Benign	-0.81	T
MutationAssessor	Uncertain	2.3	M;.
MutationTaster	Benign	0.92	N;N
PrimateAI	Benign	0.35	T
PROVEAN	Benign	-1.2	N;N
REVEL	Benign	0.11
Sift	Benign	0.33	T;T
Sift4G	Benign	0.37	T;T
Polyphen		0.99	D;.
Vest4		0.16
MVP		0.86
MPC		0.23
ClinPred		0.13	T
GERP RS		5.2
Varity_R		0.033
gMVP		0.11

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.020		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs146504061; hg19: chr15-91298049; COSMIC: COSV104665696; COSMIC: COSV104665696;