rs3797302

chr5-146509560-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001382548.1(TCERG1):c.3146+315G>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.123 in 149,830 control chromosomes in the GnomAD database, including 2,266 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 (2266 hom., cov: 30)
• Consequence: TCERG1 NM_001382548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.395

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 -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.79).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.698 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCERG1	NM_001382548.1	c.3146+315G>C		intron_variant		ENST00000679501.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCERG1	ENST00000679501.2	c.3146+315G>C		intron_variant			NM_001382548.1	A2

Frequencies

GnomAD3 genomes AF: 0.123 AC: 18388 AN: 149722 Hom.: 2269 Cov.: 30

Gnomad AFR AF: 0.0535

Gnomad AMI AF: 0.0110

Gnomad AMR AF: 0.125

Gnomad ASJ AF: 0.123

Gnomad EAS AF: 0.718

Gnomad SAS AF: 0.248

Gnomad FIN AF: 0.118

Gnomad MID AF: 0.0993

Gnomad NFE AF: 0.112

Gnomad OTH AF: 0.138

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

GnomAD4 genome AF: 0.123 AC: 18392 AN: 149830 Hom.: 2266 Cov.: 30 AF XY: 0.130 AC XY: 9475 AN XY: 72956

Gnomad4 AFR AF: 0.0534

Gnomad4 AMR AF: 0.125

Gnomad4 ASJ AF: 0.123

Gnomad4 EAS AF: 0.717

Gnomad4 SAS AF: 0.247

Gnomad4 FIN AF: 0.118

Gnomad4 NFE AF: 0.112

Gnomad4 OTH AF: 0.142

Alfa AF: 0.107 Hom.: 150

Bravo AF: 0.121

Asia WGS AF: 0.435 AC: 1503 AN: 3468

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.79
Cadd	Benign	2.0
Dann	Benign	0.69

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: rs3797302; hg19: chr5-145889123; COSMIC: COSV57035668; COSMIC: COSV57035668;