rs1555874223

Variant names:

• chr21-43063061-G-GGATCCACCCCAATGATCTGCAGAGGGCGCGGCTTCAGGGCTCAAGCCCAGCAAAAGCCCCACCTGGAT
• rs1555874223
• NM_000071.3:c.845_846insATCCAGGTGGGGCTTTTGCTGGGCTTGAGCCCTGAAGCCGCGCCCTCTGCAGATCATTGGGGTGGATC

Variant summary

Our verdict is Likely pathogenic. The variant received 6 ACMG points: 8P and 2B. PVS1 BP6_Moderate

The NM_000071.3(CBS):​c.845_846insATCCAGGTGGGGCTTTTGCTGGGCTTGAGCCCTGAAGCCGCGCCCTCTGCAGATCATTGGGGTGGATC​(p.Glu283SerfsTer9) variant causes a frameshift, stop gained change involving the alteration of a conserved nucleotide. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Likely benign (★). Synonymous variant affecting the same amino acid position (i.e. P282P) has been classified as Likely benign. Variant results in nonsense mediated mRNA decay.

• Frequency: Genomes: not found (cov: 0)
• Consequence: CBS NM_000071.3 frameshift, stop_gained
• Clinical Significance: Likely benign criteria provided, single submitter B:2
• Conservation: PhyloP100: 8.70
• Publications: 0 publications found

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]

CBS Gene-Disease associations (from GenCC):

• classic homocystinuria

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: G2P, Orphanet, Labcorp Genetics (formerly Invitae), Myriad Women’s Health, PanelApp Australia, ClinGen, Genomics England PanelApp

ACMG classification

Our verdict: Likely_pathogenic. The variant received 6 ACMG points.

• PVS1: Loss of function variant, product undergoes nonsense mediated mRNA decay. LoF is a known mechanism of disease.
• BP6: Variant 21-43063061-G-GGATCCACCCCAATGATCTGCAGAGGGCGCGGCTTCAGGGCTCAAGCCCAGCAAAAGCCCCACCTGGAT is Benign according to our data. Variant chr21-43063061-G-GGATCCACCCCAATGATCTGCAGAGGGCGCGGCTTCAGGGCTCAAGCCCAGCAAAAGCCCCACCTGGAT is described in ClinVar as Likely_benign. ClinVar VariationId is 264368.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
CBS	NM_000071.3	c.845_846insATCCAGGTGGGGCTTTTGCTGGGCTTGAGCCCTGAAGCCGCGCCCTCTGCAGATCATTGGGGTGGATC	p.Glu283SerfsTer9	frameshift_variant, stop_gained	Exon 10 of 17	ENST00000398165.8	NP_000062.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
CBS	ENST00000398165.8	c.845_846insATCCAGGTGGGGCTTTTGCTGGGCTTGAGCCCTGAAGCCGCGCCCTCTGCAGATCATTGGGGTGGATC	p.Glu283SerfsTer9	frameshift_variant, stop_gained	Exon 10 of 17	1	NM_000071.3	ENSP00000381231.4

Frequencies

GnomAD3 genomes Cov.: 0

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 0

ClinVar

Significance: Likely benign

Submissions summary: Benign:2

Revision: criteria provided, single submitter

Submissions by phenotype

Familial thoracic aortic aneurysm and aortic dissection Benign:1

Oct 11, 2018

Ambry Genetics

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

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. -

Classic homocystinuria Benign:1

Sep 16, 2020

Natera, Inc.

Significance: Likely benign

Review Status: no assertion criteria provided

Collection Method: clinical testing

- -

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
PhyloP100		8.7

Splicing

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

Other links and lift over

dbSNP: rs1555874223; hg19: chr21-44483171;