chr1-167439354-TG-CA

Variant names:

• chr1-167439354-TG-CA
• rs193922739
• NM_198053.3:c.208_209delCAinsTG

Variant summary

Our verdict is Uncertain significance. The variant received 3 ACMG points: 3P and 0B. PM5 PP5

The NM_198053.3(CD247):​c.208_209delCAinsTG​(p.Gln70Trp) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type MNV, and the frequency of such variant types in population databases may be underestimated and unreliable. Variant has been reported in ClinVar as Pathogenic (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. Q70Y) has been classified as Pathogenic.

• Frequency: Genomes: not found (cov: 33)
• Consequence: CD247 NM_198053.3 missense
• Clinical Significance: Pathogenic no assertion criteria provided P:1
• Conservation: PhyloP100: 2.97
• Publications: 1 publications found

Genes affected

CD247 (HGNC:1677): (CD247 molecule) The protein encoded by this gene is T-cell receptor zeta, which together with T-cell receptor alpha/beta and gamma/delta heterodimers, and with CD3-gamma, -delta and -epsilon, forms the T-cell receptor-CD3 complex. The zeta chain plays an important role in coupling antigen recognition to several intracellular signal-transduction pathways. Low expression of the antigen results in impaired immune response. Two alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

CD247 Gene-Disease associations (from GenCC):

• immunodeficiency 25

  Inheritance: AR Classification: DEFINITIVE, STRONG, LIMITED Submitted by: Labcorp Genetics (formerly Invitae), ClinGen, Ambry Genetics
• T-B+ severe combined immunodeficiency due to CD3delta/CD3epsilon/CD3zeta

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Uncertain_significance. The variant received 3 ACMG points.

• PM5: Other missense variant is known to change same aminoacid residue: Variant chr1-167439353-CTG-ATA is described in ClinVar as Pathogenic. ClinVar VariationId is 12752.Status of the report is no_assertion_criteria_provided, 0 stars.
• PP5: Variant 1-167439354-TG-CA is Pathogenic according to our data. Variant chr1-167439354-TG-CA is described in ClinVar as Pathogenic. ClinVar VariationId is 12750.Status of the report is no_assertion_criteria_provided, 0 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_198053.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD247	NM_198053.3	MANE Select	c.208_209delCAinsTG	p.Gln70Trp	missense	N/A	NP_932170.1
	CD247	NM_001378515.1		c.301_302delCAinsTG	p.Gln101Trp	missense	N/A	NP_001365444.1
	CD247	NM_001378516.1		c.301_302delCAinsTG	p.Gln101Trp	missense	N/A	NP_001365445.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	CD247	ENST00000362089.10	TSL:1 MANE Select	c.208_209delCAinsTG	p.Gln70Trp	missense	N/A	ENSP00000354782.5
	CD247	ENST00000392122.4	TSL:1	c.208_209delCAinsTG	p.Gln70Trp	missense	N/A	ENSP00000375969.3
	CD247	ENST00000470379.2	TSL:1	c.-78_-77delCAinsTG		5_prime_UTR	Exon 1 of 6	ENSP00000514807.1

Frequencies

GnomAD3 genomes Cov.: 33

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 33

ClinVar

ClinVar submissions as Germline

Significance: Pathogenic

Revision: no assertion criteria provided

Pathogenic	VUS	Benign	Condition
1	-	-	Immunodeficiency 25 (1)

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		3.0

Splicing

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

Other links and lift over

dbSNP: rs193922739; hg19: chr1-167408591;