chr1-167431429-TACCTGCACC-T

Position:

• chr1-167431429-TACCTGCACC-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_Moderate BA1

The NM_198053.3(CD247):​c.*243_*251del variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0387 in 605,558 control chromosomes in the GnomAD database, including 589 homozygotes. Variant has been reported in ClinVar as Likely benign (★).

• Frequency:
  • Genomes: 𝑓 0.035 (122 hom., cov: 32)
  • Exomes 𝑓: 0.040 (467 hom.)
• Consequence: CD247 NM_198053.3 3_prime_UTR
• Clinical Significance: Likely benign criteria provided, single submitter B:1
• Conservation: PhyloP100: 1.16

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]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP6: Variant 1-167431429-TACCTGCACC-T is Benign according to our data. Variant chr1-167431429-TACCTGCACC-T is described in ClinVar as [Likely_benign]. Clinvar id is 1223432.Status of the report is criteria_provided_single_submitter, 1 stars.
• BA1: GnomAdExome4 highest subpopulation (MID) allele frequency at 95% confidence interval = 0.0672 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
CD247	NM_198053.3	c.*243_*251del		3_prime_UTR_variant	8/8	ENST00000362089.10

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
CD247	ENST00000362089.10	c.*243_*251del		3_prime_UTR_variant	8/8	1	NM_198053.3	A1

Frequencies

GnomAD3 genomes AF: 0.0350 AC: 5328 AN: 152192 Hom.: 122 Cov.: 32

Gnomad AFR AF: 0.0182

Gnomad AMI AF: 0.0482

Gnomad AMR AF: 0.0349

Gnomad ASJ AF: 0.0683

Gnomad EAS AF: 0.000385

Gnomad SAS AF: 0.0292

Gnomad FIN AF: 0.0231

Gnomad MID AF: 0.0696

Gnomad NFE AF: 0.0478

Gnomad OTH AF: 0.0449

GnomAD4 exome AF: 0.0400 AC: 18126 AN: 453248 Hom.: 467 AF XY: 0.0397 AC XY: 9493 AN XY: 239414

Gnomad4 AFR exome AF: 0.0172

Gnomad4 AMR exome AF: 0.0296

Gnomad4 ASJ exome AF: 0.0660

Gnomad4 EAS exome AF: 0.0000320

Gnomad4 SAS exome AF: 0.0276

Gnomad4 FIN exome AF: 0.0280

Gnomad4 NFE exome AF: 0.0477

Gnomad4 OTH exome AF: 0.0440

GnomAD4 genome AF: 0.0350 AC: 5327 AN: 152310 Hom.: 122 Cov.: 32 AF XY: 0.0331 AC XY: 2468 AN XY: 74470

Gnomad4 AFR AF: 0.0182

Gnomad4 AMR AF: 0.0348

Gnomad4 ASJ AF: 0.0683

Gnomad4 EAS AF: 0.000386

Gnomad4 SAS AF: 0.0296

Gnomad4 FIN AF: 0.0231

Gnomad4 NFE AF: 0.0478

Gnomad4 OTH AF: 0.0440

Alfa AF: 0.0399 Hom.: 14

Bravo AF: 0.0351

Asia WGS AF: 0.0100 AC: 36 AN: 3478

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

Submissions by phenotype

not provided Benign:1

Likely benign, criteria provided, single submitter

clinical testing

GeneDx

Aug 10, 2018

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Computational scores

Source: dbNSFP v4.3

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs34484379; hg19: chr1-167400666;