rs375846341

chr21-43058970-T-G

Variant summary

Our verdict is Pathogenic. Variant got 14 ACMG points: 14P and 0B. PVS1_Moderate PP3_Strong PP5_Very_Strong

The NM_000071.3(CBS):c.1224-2A>C variant causes a splice acceptor change involving the alteration of a conserved nucleotide. In-silico tool predicts a pathogenic outcome for this variant. 2/2 splice prediction tools predicting alterations to normal splicing. Variant has been reported in ClinVar as Pathogenic (★★).

• Frequency: Genomes: not found (cov: 0)
• Consequence: CBS NM_000071.3 splice_acceptor
• Scores: Splicing: ADA: 1.000
• Clinical Significance: Pathogenic criteria provided, multiple submitters, no conflicts P:17
• Conservation: PhyloP100: 7.60

Genes affected

CBS (HGNC:1550): (cystathionine beta-synthase) The protein encoded by this gene acts as a homotetramer to catalyze the conversion of homocysteine to cystathionine, the first step in the transsulfuration pathway. The encoded protein is allosterically activated by adenosyl-methionine and uses pyridoxal phosphate as a cofactor. Defects in this gene can cause cystathionine beta-synthase deficiency (CBSD), which can lead to homocystinuria. This gene is a major contributor to cellular hydrogen sulfide production. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Feb 2016]

ACMG classification

Verdict is Pathogenic. Variant got 14 ACMG points.

• PVS1: Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.08091787 fraction of the gene. Cryptic splice site detected, with MaxEntScore 5.8, offset of 22, new splice context is: ggtggcacctccgtgttcAGgag. Cryptic site results in frameshift change. If cryptic site found is not functional and variant results in exon loss, it results in inframe change.
• PP3: Splicing scoreres supports a deletorius effect: Scorers claiming Pathogenic: dbscSNV1_ADA, dbscSNV1_RF. No scorers claiming Uncertain. No scorers claiming Benign.
• PP5: Variant 21-43058970-T-G is Pathogenic according to our data. Variant chr21-43058970-T-G is described in ClinVar as [Pathogenic]. Clinvar id is 128.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr21-43058970-T-G is described in Lovd as [Pathogenic].

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CBS	NM_000071.3	c.1224-2A>C		splice_acceptor_variant		ENST00000398165.8

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CBS	ENST00000398165.8	c.1224-2A>C		splice_acceptor_variant		1	NM_000071.3	P1

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD3 exomes AF: 0.0000785 AC: 17 AN: 216552 Hom.: 0 AF XY: 0.0000766 AC XY: 9 AN XY: 117434

Gnomad AFR exome AF: 0.00

Gnomad AMR exome AF: 0.00

Gnomad ASJ exome AF: 0.00139

Gnomad EAS exome AF: 0.00

Gnomad SAS exome AF: 0.00

Gnomad FIN exome AF: 0.00

Gnomad NFE exome AF: 0.0000409

Gnomad OTH exome AF: 0.00

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

Alfa AF: 0.000197 Hom.: 0

ESP6500AA AF: 0.00 AC: 0

ESP6500EA AF: 0.000117 AC: 1

ExAC AF: 0.0000661 AC: 8

ClinVar

Significance: Pathogenic

Submissions summary: Pathogenic:17

Revision: criteria provided, multiple submitters, no conflicts

Submissions by phenotype

Classic homocystinuria Pathogenic:9

Pathogenic, criteria provided, single submitter	clinical testing	Fulgent Genetics, Fulgent Genetics	Aug 25, 2021	- -
Pathogenic, no assertion criteria provided	clinical testing	Child Health and Human Development Program, Research Institute of the McGill University Health Center	-	The IVS11-2 A>C (also c.1224-2A>C) was identified in two patients of Eastern European origin in compound heterozygote with c.833C>T (I278T) in one of the patients and c.430G>C (E144Q) in the other. Clinical characteristics in both patients included lens dislocation and elevated fasting homocysteine. Patients had no intellectual impairment and do not respond to treatment with vitamin B6. -
Pathogenic, criteria provided, single submitter	clinical testing	Revvity Omics, Revvity	Jun 19, 2023	- -
Pathogenic, criteria provided, single submitter	clinical testing	Centre for Mendelian Genomics, University Medical Centre Ljubljana	Oct 24, 2019	This variant was classified as: Pathogenic. The following ACMG criteria were applied in classifying this variant: PVS1,PS1,PM2. -
Pathogenic, criteria provided, single submitter	clinical testing	3billion	Sep 01, 2022	The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: 0.008%). This variant on the canonical splice site is predicted to alter splicing, resulting in a loss or disruption of normal protein function. Multiple pathogenic loss-of-function variants are reported downstream of the variant. The variant has been reported at least twice as pathogenic with clinical assertions and evidence for the classification (ClinVar ID: VCV000000128). Therefore, this variant is classified as Pathogenic according to the recommendation of ACMG/AMP guideline. -
Pathogenic, criteria provided, single submitter	clinical testing	Illumina Laboratory Services, Illumina	Sep 21, 2018	The CBS c.1224-2A>C variant, which occurs in a canonical splice acceptor site, has been reported in seven studies and is found in a total of 33 individuals with homocystinuria, including three homozygotes, 28 compound heterozygotes, and two heterozygotes (Kozich et al. 1992; Janosik et al. 2001; Orendae et al. 2004; Linnebank et al. 2004; Magner et al. 2011; Karaca et al. 2014; Alcaide et al. 2015). Control data are unavailable for this variant, which is reported at a frequency of 0.0003 in the European (non-Finnish) population of the Exome Aggregation Consortium. The c.1224-2A>C variant was found to cause an in-frame deletion of exon 12 and result in an inactive protein (Kozich et al. 1992). Functional studies in E. coli confirmed that the c.1224-2A>C variant results in an inactive enzyme (Janosik et al. 2001; Orendae et al. 2004), and CBS activity in cultured skin fibroblasts from probands carrying this variant was significantly reduced compared to wild type (Janosik et al. 2001). Based on the collective evidence and the potential impact of splice acceptor variants, the c.1224-2A>C variant is classified as pathogenic for homocystinuria. This variant was observed by ICSL as part of a predisposition screen in an ostensibly healthy population. -
Pathogenic, criteria provided, single submitter	clinical testing	Baylor Genetics	Oct 11, 2023	- -
Pathogenic, no assertion criteria provided	clinical testing	Natera, Inc.	Sep 16, 2020	- -
Pathogenic, criteria provided, single submitter	clinical testing	Myriad Genetics, Inc.	Nov 09, 2021	NM_000071.2(CBS):c.1224-2A>C is a canonical splice variant classified as pathogenic in the context of homocystinuria, CBS-related. c.1224-2A>C has been observed in cases with relevant disease (PMID: 15365998). Functional assessments of this variant are available in the literature (PMID: 20506325, 20490928). c.1224-2A>C has been observed in population frequency databases (gnomAD: ASJ 0.14%). In summary, NM_000071.2(CBS):c.1224-2A>C is a canonical splice variant that has been observed more frequently in cases with the relevant disease than in healthy populations. Please note: this variant was assessed in the context of healthy population screening. -

not provided Pathogenic:3

Pathogenic, criteria provided, single submitter	clinical testing	GeneDx	Jul 07, 2023	Segregates with disease in affected individuals from a single family in published literature (Orendae et al., 2004); Published functional studies demonstrate decreases enzyme activity (Kozich et al., 1992; Kopeck et al., 2011; Alcaide et al., 2015); Canonical splice site variant predicted to result in an in-frame loss of the adjacent exon in a gene for which loss of function is a known mechanism of disease; This variant is associated with the following publications: (PMID: 24211323, 21030686, 1301198, 27059523, 20567906, 25525159, 15365998, 20490928, 20506325, 15146473, 11359213, 32232970, 25218699) -
Pathogenic, criteria provided, single submitter	clinical testing	CeGaT Center for Human Genetics Tuebingen	Jul 01, 2023	CBS: PVS1:Strong, PM2, PM3, PP4, PS3:Supporting -
Pathogenic, criteria provided, single submitter	clinical testing	Eurofins Ntd Llc (ga)	Jun 02, 2015	- -

Homocystinuria, pyridoxine-responsive Pathogenic:1

Pathogenic, no assertion criteria provided

literature only

OMIM

Jan 01, 1992

- -

CBS-related condition Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

PreventionGenetics, part of Exact Sciences

Jan 18, 2024

The CBS c.1224-2A>C variant is predicted to disrupt the AG splice acceptor site and interfere with normal splicing. This variant has been reported in the homozygous state or with a second CBS variant in individuals with homocystinuria, and has been shown to cause skipping of exon 14 (for example, see Kozich et al 1992. PubMed ID: 1301198; Linnebank et al. 2004. PubMed ID: 15365998; Kopecká et al 2010. PubMed ID: 20490928). In at least one individual, this variant was shown by family segregation studies to be on the opposite allele as a known pathogenic variant in CBS (Kozich et al 1992. PubMed ID: 1301198). This variant is reported in 0.14% of alleles in individuals of Ashkenazi Jewish descent in gnomAD. Variants that disrupt the consensus splice acceptor site in CBS are expected to be pathogenic. This variant is interpreted as pathogenic. -

Familial thoracic aortic aneurysm and aortic dissection Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Ambry Genetics

Nov 24, 2020

The c.1224-2A>C intronic pathogenic mutation results from an A to C substitution two nucleotides upstream from coding exon 12 in the CBS gene. This alteration has been reported with p.I278T in a subject with homocystinuria (Kozich V et al. Hum Mutat, 1992;1:113-23). In silico splice site analysis predicts that this alteration will weaken the native splice acceptor site and will result in the creation or strengthening of a novel splice acceptor site. Alterations that disrupt the canonical splice site are expected to cause aberrant splicing, resulting in an abnormal protein or a transcript that is subject to nonsense-mediated mRNA decay. As such, this alteration is classified as a disease-causing mutation. -

HYPERHOMOCYSTEINEMIA, THROMBOTIC, CBS-RELATED Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Invitae

Dec 19, 2023

This sequence change affects an acceptor splice site in intron 13 of the CBS gene. RNA analysis indicates that disruption of this splice site induces altered splicing and likely results in a shortened protein product. This variant is present in population databases (rs375846341, gnomAD 0.1%). Disruption of this splice site has been observed in individual(s) with homocystinuria (PMID: 1301198, 11359213, 15146473, 15365998, 20567906). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. It has also been observed to segregate with disease in related individuals. This variant is also known as IVS11-2A>C or p.W409_G453del. ClinVar contains an entry for this variant (Variation ID: 128). Studies have shown that disruption of this splice site results in skipping of exon 14, but is expected to preserve the integrity of the reading-frame (PMID: 1301198, 20490928, 20506325). For these reasons, this variant has been classified as Pathogenic. -

Homocystinuria Pathogenic:1

Pathogenic, criteria provided, single submitter

clinical testing

Women's Health and Genetics/Laboratory Corporation of America, LabCorp

Mar 27, 2017

Variant summary: The CBS c.1224-2A>C variant (alternatively also known as IVS11-2A>C) involves the alteration of a highly conserved intronic nucleotide in the canonical splice acceptor site in intron 13, and is expected to cause aberrant gene splicing. 5/5 splice prediction tools also predict abrogation of the splice acceptor site. Consistent to these predictions, this variant is shown to cause exon skipping resulting in an in-frame deletion of exon 12 (amino acids W408 to G453) (Kozick_1992); exon 12 is involved in encoding the CBS domain of the protein (InterPro). In addition, expression of this variant in bacterial (E. coli) system shows that this variant not only leads to abrogation of catalytic activity, but also non-responsiveness to chaperones used to treat the CBS deficiency (Orendac _2004, Kopecka_2011). This variant was found in 7/45474 control chromosomes from ExAC at a frequency of 0.0001539, which does not exceed the estimated maximal expected allele frequency of a pathogenic CBS variant (0.0030414). This variant has been reported in several patients with CBS deficiency in homozygous as well as compound heterozygous with other pathogenic or potentially pathogenic variants including evidence of cosegregation with disease. It is predominantly found in patients from Central Europe, where it has been found on in average 14% of mutant alleles with evidence of founder effect (Linnebank_2004). Available patient and functional data indicate that this variant is likely a severe mutation. Multiple clinical diagnostic laboratories/reputable databases have classified this variant as pathogenic. Taken together, this variant is classified as Pathogenic. -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_addAF	Pathogenic	0.20	D
BayesDel_noAF	Pathogenic	0.18
Cadd	Pathogenic	35
Dann	Uncertain	0.99
Eigen	Pathogenic	1.0
Eigen_PC	Pathogenic	0.84
FATHMM_MKL	Uncertain	0.97	D
MutationTaster	Benign	1.0	D;D;D;D;D;D;D;D;D;D;D;D
GERP RS		4.5

Splicing

Name	Calibrated prediction	Score	Prediction
dbscSNV1_ADA	Pathogenic	1.0
dbscSNV1_RF	Pathogenic	0.93
SpliceAI score (max)		0.99		Details are displayed if max score is > 0.2
DS_AG_spliceai		0.85		Position offset: -24
DS_AL_spliceai		0.99		Position offset: -2

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

Publications

LitVar

Other links and lift over

dbSNP: rs375846341; hg19: chr21-44479080;