Genetic Variant ENST00000506524.5:n.3171C>T (chr5-146510892-C-T) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. The variant received -10 ACMG points: 0P and 10B. BP4_ModerateBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.983

Publications

16 publications found

Variant links:

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]

TCERG1 links:

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ACMG classification

Classification was made for transcript

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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCERG1	NM_001382548.1 link	c.*250C>T		3_prime_UTR_variant	Exon 23 of 23	ENST00000679501.2	NP_001369477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCERG1	ENST00000679501.2 link	c.*250C>T		3_prime_UTR_variant	Exon 23 of 23		NM_001382548.1	ENSP00000505217.1		A0A7P0T8N8

Frequencies

GnomAD3 genomes

AF:

0.122

AC:

18507

AN:

152050

Hom.:

2291

Cov.:

show subpopulations

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.:

AF XY:

0.167

AC XY:

13638

AN XY:

81634

show subpopulations

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

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.509

Heterozygous variant carriers

849

1698

2547

3396

4245

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

252

378

504

630

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

GnomAD4 genome

AF:

0.122

AC:

18510

AN:

152168

Hom.:

2288

Cov.:

AF XY:

0.129

AC XY:

9562

AN XY:

74406

show subpopulations

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:

AN:

294

European-Non Finnish (NFE)

AF:

0.111

AC:

7563

AN:

67988

Other (OTH)

AF:

0.140

AC:

295

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

705

1409

2114

2818

3523

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

212

424

636

848

1060

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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 v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.44

CADD

Benign

(source)

DANN

Benign

0.82

PhyloP100

0.98

Mutation Taster

=100/0

polymorphism (auto)

(source)

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

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over