rs1370868

Variant names:

• chr10-131186093-G-A
• rs1370868
• NM_174937.4:c.857-19208C>T

Variant summary

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

The NM_174937.4(TCERG1L):​c.857-19208C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.754 in 152,110 control chromosomes in the GnomAD database, including 44,740 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 0.75 (44740 hom., cov: 33)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.944
• Publications: 3 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 (SAS) allele frequency at 95% confidence interval = 0.882 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	NM_174937.4	MANE Select	c.857-19208C>T		intron	N/A	NP_777597.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	ENST00000368642.4	TSL:1 MANE Select	c.857-19208C>T		intron	N/A	ENSP00000357631.4
	TCERG1L	ENST00000483040.1	TSL:5	n.79-19208C>T		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.754 AC: 114572 AN: 151992 Hom.: 44716 Cov.: 33

Gnomad AFR AF: 0.535

Gnomad AMI AF: 0.896

Gnomad AMR AF: 0.765

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.778

Gnomad SAS AF: 0.903

Gnomad FIN AF: 0.823

Gnomad MID AF: 0.835

Gnomad NFE AF: 0.852

Gnomad OTH AF: 0.779

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

GnomAD4 genome AF: 0.754 AC: 114644 AN: 152110 Hom.: 44740 Cov.: 33 AF XY: 0.754 AC XY: 56074 AN XY: 74362

African (AFR) AF: 0.536 AC: 22198 AN: 41450

American (AMR) AF: 0.765 AC: 11685 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3007 AN: 3468

East Asian (EAS) AF: 0.778 AC: 4013 AN: 5158

South Asian (SAS) AF: 0.905 AC: 4367 AN: 4828

European-Finnish (FIN) AF: 0.823 AC: 8711 AN: 10584

Middle Eastern (MID) AF: 0.840 AC: 247 AN: 294

European-Non Finnish (NFE) AF: 0.852 AC: 57948 AN: 68020

Other (OTH) AF: 0.780 AC: 1651 AN: 2116

Alfa AF: 0.712 Hom.: 16187

Bravo AF: 0.736

Asia WGS AF: 0.851 AC: 2957 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	0.41
DANN	Benign	0.53
PhyloP100		-0.94
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: rs1370868; hg19: chr10-132984356;