5-146510892-C-T

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The NM_001382548.1(TCERG1):c.*250C>T variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.145 in 311,938 control chromosomes in the GnomAD database, including 7,024 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency:
  • Genomes: 𝑓 0.12 (2288 hom., cov: 32)
  • Exomes 𝑓: 0.17 (4736 hom.)
• Consequence: TCERG1 NM_001382548.1 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.983

Genes affected

TCERG1 (HGNC:15630): (transcription elongation regulator 1) This gene encodes a nuclear protein that regulates transcriptional elongation and pre-mRNA splicing. The encoded protein interacts with the hyperphosphorylated C-terminal domain of RNA polymerase II via multiple FF domains, and with the pre-mRNA splicing factor SF1 via a WW domain. Alternative splicing results in multiple transcripts variants encoding different isoforms. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Benign. Variant got -10 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.44).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.699 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCERG1	NM_001382548.1	c.*250C>T		3_prime_UTR_variant	23/23	ENST00000679501.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCERG1	ENST00000679501.2	c.*250C>T		3_prime_UTR_variant	23/23		NM_001382548.1	A2

Frequencies

GnomAD3 genomes AF: 0.122 AC: 18507 AN: 152050 Hom.: 2291 Cov.: 32

Gnomad AFR AF: 0.0529

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.124

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.719

Gnomad SAS AF: 0.245

Gnomad FIN AF: 0.115

Gnomad MID AF: 0.0981

Gnomad NFE AF: 0.111

Gnomad OTH AF: 0.135

GnomAD4 exome AF: 0.168 AC: 26784 AN: 159770 Hom.: 4736 Cov.: 3 AF XY: 0.167 AC XY: 13638 AN XY: 81634

Gnomad4 AFR exome AF: 0.0548

Gnomad4 AMR exome AF: 0.104

Gnomad4 ASJ exome AF: 0.123

Gnomad4 EAS exome AF: 0.746

Gnomad4 SAS exome AF: 0.202

Gnomad4 FIN exome AF: 0.116

Gnomad4 NFE exome AF: 0.114

Gnomad4 OTH exome AF: 0.150

GnomAD4 genome AF: 0.122 AC: 18510 AN: 152168 Hom.: 2288 Cov.: 32 AF XY: 0.129 AC XY: 9562 AN XY: 74406

Gnomad4 AFR AF: 0.0527

Gnomad4 AMR AF: 0.124

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.718

Gnomad4 SAS AF: 0.244

Gnomad4 FIN AF: 0.115

Gnomad4 NFE AF: 0.111

Gnomad4 OTH AF: 0.140

Alfa AF: 0.111 Hom.: 1078

Bravo AF: 0.121

Asia WGS AF: 0.436 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
Cadd	Benign	13
Dann	Benign	0.82

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		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: rs3822506; hg19: chr5-145890455; COSMIC: COSV57035683; COSMIC: COSV57035683;