ENST00000506524.5:n.3171C>T

Variant names:

• chr5-146510892-C-T
• rs3822506
• ENST00000506524.5:n.3171C>T

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_Moderate BA1

The ENST00000506524.5(TCERG1):​n.3171C>T variant causes a non coding transcript exon 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 ENST00000506524.5 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.983
• Publications: 16 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 -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000506524.5. 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.*250C>T		3_prime_UTR	Exon 23 of 23	NP_001369477.1
	TCERG1	NR_174389.1		n.3658C>T		non_coding_transcript_exon	Exon 23 of 23
	TCERG1	NR_174390.1		n.3647C>T		non_coding_transcript_exon	Exon 22 of 22

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1	ENST00000506524.5	TSL:1	n.3171C>T		non_coding_transcript_exon	Exon 11 of 11
	TCERG1	ENST00000679501.2	MANE Select	c.*250C>T		3_prime_UTR	Exon 23 of 23	ENSP00000505217.1
	TCERG1	ENST00000296702.9	TSL:1	c.*250C>T		3_prime_UTR	Exon 22 of 22	ENSP00000296702.5

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

African (AFR) AF: 0.0548 AC: 300 AN: 5472

American (AMR) AF: 0.104 AC: 567 AN: 5430

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 753 AN: 6140

East Asian (EAS) AF: 0.746 AC: 9392 AN: 12598

South Asian (SAS) AF: 0.202 AC: 1224 AN: 6060

European-Finnish (FIN) AF: 0.116 AC: 1158 AN: 9956

Middle Eastern (MID) AF: 0.134 AC: 109 AN: 816

European-Non Finnish (NFE) AF: 0.114 AC: 11685 AN: 102654

Other (OTH) AF: 0.150 AC: 1596 AN: 10644

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

African (AFR) AF: 0.0527 AC: 2191 AN: 41550

American (AMR) AF: 0.124 AC: 1894 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 427 AN: 3470

East Asian (EAS) AF: 0.718 AC: 3709 AN: 5166

South Asian (SAS) AF: 0.244 AC: 1174 AN: 4808

European-Finnish (FIN) AF: 0.115 AC: 1215 AN: 10580

Middle Eastern (MID) AF: 0.109 AC: 32 AN: 294

European-Non Finnish (NFE) AF: 0.111 AC: 7563 AN: 67988

Other (OTH) AF: 0.140 AC: 295 AN: 2112

Alfa AF: 0.109 Hom.: 1376

Bravo AF: 0.121

Asia WGS AF: 0.436 AC: 1510 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.44
CADD	Benign	13
DANN	Benign	0.82
PhyloP100		0.98
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs3822506; hg19: chr5-145890455; COSMIC: COSV57035683; COSMIC: COSV57035683;