5-146472334-C-T

Variant names:

• chr5-146472334-C-T
• rs2400219
• NM_001382548.1:c.1601+758C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001382548.1(TCERG1):​c.1601+758C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.245 in 151,736 control chromosomes in the GnomAD database, including 5,645 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 0.24 (5645 hom., cov: 31)
• Consequence: TCERG1 NM_001382548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -4.92
• Publications: 3 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.05).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.814 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001382548.1. 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
	TCERG1	NM_001382548.1	MANE Select	c.1601+758C>T		intron	N/A	NP_001369477.1
	TCERG1	NM_006706.4		c.1601+758C>T		intron	N/A	NP_006697.2
	TCERG1	NM_001400082.1		c.1544+758C>T		intron	N/A	NP_001387011.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1	ENST00000679501.2	MANE Select	c.1601+758C>T		intron	N/A	ENSP00000505217.1
	TCERG1	ENST00000296702.9	TSL:1	c.1601+758C>T		intron	N/A	ENSP00000296702.5
	TCERG1	ENST00000394421.7	TSL:1	c.1538+758C>T		intron	N/A	ENSP00000377943.2

Frequencies

GnomAD3 genomes AF: 0.245 AC: 37098 AN: 151618 Hom.: 5642 Cov.: 31

Gnomad AFR AF: 0.252

Gnomad AMI AF: 0.140

Gnomad AMR AF: 0.229

Gnomad ASJ AF: 0.203

Gnomad EAS AF: 0.835

Gnomad SAS AF: 0.308

Gnomad FIN AF: 0.249

Gnomad MID AF: 0.152

Gnomad NFE AF: 0.198

Gnomad OTH AF: 0.254

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

GnomAD4 genome AF: 0.245 AC: 37123 AN: 151736 Hom.: 5645 Cov.: 31 AF XY: 0.252 AC XY: 18644 AN XY: 74114

African (AFR) AF: 0.251 AC: 10403 AN: 41364

American (AMR) AF: 0.229 AC: 3497 AN: 15246

Ashkenazi Jewish (ASJ) AF: 0.203 AC: 704 AN: 3468

East Asian (EAS) AF: 0.835 AC: 4288 AN: 5138

South Asian (SAS) AF: 0.308 AC: 1473 AN: 4784

European-Finnish (FIN) AF: 0.249 AC: 2629 AN: 10544

Middle Eastern (MID) AF: 0.167 AC: 49 AN: 294

European-Non Finnish (NFE) AF: 0.198 AC: 13407 AN: 67876

Other (OTH) AF: 0.258 AC: 545 AN: 2110

Alfa AF: 0.208 Hom.: 1838

Bravo AF: 0.249

Asia WGS AF: 0.542 AC: 1878 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.1
CADD	Benign	0.42
DANN	Benign	0.22
PhyloP100		-4.9
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.030		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs2400219; hg19: chr5-145851897; COSMIC: COSV57035274; COSMIC: COSV57035274;