rs1583670

Variant names:

• chr10-131185951-T-C
• rs1583670
• NM_174937.4:c.857-19066A>G

Variant summary

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

The NM_174937.4(TCERG1L):​c.857-19066A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.718 in 152,130 control chromosomes in the GnomAD database, including 41,678 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 0.72 (41678 hom., cov: 33)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.95
• Publications: 5 publications found

Genes affected

TCERG1L (HGNC:23533): (transcription elongation regulator 1 like) Predicted to enable RNA polymerase binding activity and transcription coregulator activity. Predicted to be involved in regulation of transcription, DNA-templated. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.0).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.843 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174937.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	NM_174937.4	MANE Select	c.857-19066A>G		intron	N/A	NP_777597.2	Q5VWI1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	ENST00000368642.4	TSL:1 MANE Select	c.857-19066A>G		intron	N/A	ENSP00000357631.4	Q5VWI1
	TCERG1L	ENST00000935680.1		c.857-19066A>G		intron	N/A	ENSP00000605739.1
	TCERG1L	ENST00000483040.1	TSL:5	n.79-19066A>G		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.719 AC: 109241 AN: 152012 Hom.: 41679 Cov.: 33

Gnomad AFR AF: 0.438

Gnomad AMI AF: 0.895

Gnomad AMR AF: 0.748

Gnomad ASJ AF: 0.860

Gnomad EAS AF: 0.750

Gnomad SAS AF: 0.805

Gnomad FIN AF: 0.813

Gnomad MID AF: 0.813

Gnomad NFE AF: 0.848

Gnomad OTH AF: 0.750

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

GnomAD4 genome AF: 0.718 AC: 109269 AN: 152130 Hom.: 41678 Cov.: 33 AF XY: 0.718 AC XY: 53365 AN XY: 74352

African (AFR) AF: 0.437 AC: 18127 AN: 41456

American (AMR) AF: 0.748 AC: 11424 AN: 15272

Ashkenazi Jewish (ASJ) AF: 0.860 AC: 2982 AN: 3466

East Asian (EAS) AF: 0.750 AC: 3882 AN: 5178

South Asian (SAS) AF: 0.806 AC: 3880 AN: 4814

European-Finnish (FIN) AF: 0.813 AC: 8616 AN: 10592

Middle Eastern (MID) AF: 0.816 AC: 240 AN: 294

European-Non Finnish (NFE) AF: 0.848 AC: 57718 AN: 68030

Other (OTH) AF: 0.749 AC: 1584 AN: 2116

Alfa AF: 0.790 Hom.: 39214

Bravo AF: 0.699

Asia WGS AF: 0.755 AC: 2626 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.61
DANN	Benign	0.26
PhyloP100		-2.0
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: rs1583670; hg19: chr10-132984214;