chr5-146509560-G-C

Variant names:

• chr5-146509560-G-C
• rs3797302
• NM_001382548.1:c.3146+315G>C

Variant summary

Our verdict is Benign. The variant received -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

Our verdict: Benign. The variant received -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 rank	MANE	Protein	UniProt
TCERG1	NM_001382548.1	c.3146+315G>C		intron_variant	Intron 22 of 22	ENST00000679501.2	NP_001369477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCERG1	ENST00000679501.2	c.3146+315G>C		intron_variant	Intron 22 of 22		NM_001382548.1	ENSP00000505217.1

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

African (AFR) AF: 0.0534 AC: 2168 AN: 40622

American (AMR) AF: 0.125 AC: 1887 AN: 15060

Ashkenazi Jewish (ASJ) AF: 0.123 AC: 424 AN: 3454

East Asian (EAS) AF: 0.717 AC: 3676 AN: 5124

South Asian (SAS) AF: 0.247 AC: 1175 AN: 4750

European-Finnish (FIN) AF: 0.118 AC: 1172 AN: 9912

Middle Eastern (MID) AF: 0.113 AC: 32 AN: 282

European-Non Finnish (NFE) AF: 0.112 AC: 7553 AN: 67638

Other (OTH) AF: 0.142 AC: 295 AN: 2080

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
PhyloP100		0.40
Mutation Taster		=99/1	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

Publications

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Other links and lift over

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