rs17104665

Variant names:

• chr5-146462906-A-G
• rs17104665
• NM_001382548.1:c.893-645A>G

Variant summary

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

The NM_001382548.1(TCERG1):​c.893-645A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0954 in 152,240 control chromosomes in the GnomAD database, including 874 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 0.095 (874 hom., cov: 32)
• Consequence: TCERG1 NM_001382548.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.93
• Publications: 2 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=-0.83).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.16 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCERG1	NM_001382548.1	c.893-645A>G		intron_variant	Intron 4 of 22	ENST00000679501.2	NP_001369477.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCERG1	ENST00000679501.2	c.893-645A>G		intron_variant	Intron 4 of 22		NM_001382548.1	ENSP00000505217.1

Frequencies

GnomAD3 genomes AF: 0.0953 AC: 14497 AN: 152122 Hom.: 869 Cov.: 32

Gnomad AFR AF: 0.163

Gnomad AMI AF: 0.0548

Gnomad AMR AF: 0.0958

Gnomad ASJ AF: 0.105

Gnomad EAS AF: 0.00115

Gnomad SAS AF: 0.0543

Gnomad FIN AF: 0.0328

Gnomad MID AF: 0.123

Gnomad NFE AF: 0.0739

Gnomad OTH AF: 0.0937

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

GnomAD4 genome AF: 0.0954 AC: 14521 AN: 152240 Hom.: 874 Cov.: 32 AF XY: 0.0921 AC XY: 6859 AN XY: 74444

African (AFR) AF: 0.163 AC: 6771 AN: 41510

American (AMR) AF: 0.0956 AC: 1463 AN: 15296

Ashkenazi Jewish (ASJ) AF: 0.105 AC: 365 AN: 3470

East Asian (EAS) AF: 0.00116 AC: 6 AN: 5190

South Asian (SAS) AF: 0.0539 AC: 260 AN: 4822

European-Finnish (FIN) AF: 0.0328 AC: 348 AN: 10620

Middle Eastern (MID) AF: 0.119 AC: 35 AN: 294

European-Non Finnish (NFE) AF: 0.0739 AC: 5027 AN: 68012

Other (OTH) AF: 0.0927 AC: 196 AN: 2114

Alfa AF: 0.0858 Hom.: 129

Bravo AF: 0.105

Asia WGS AF: 0.0390 AC: 137 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.83
CADD	Benign	7.5
DANN	Benign	0.69
PhyloP100		1.9
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: rs17104665; hg19: chr5-145842469;