rs1370868

Positions:

• chr10-131186093-G-A

Variant summary

Our verdict is Benign. Variant got -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

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

Verdict is Benign. Variant got -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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCERG1L	NM_174937.4	c.857-19208C>T		intron_variant		ENST00000368642.4
TCERG1L	XM_047424966.1	c.857-19208C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCERG1L	ENST00000368642.4	c.857-19208C>T		intron_variant		1	NM_174937.4	P1
TCERG1L	ENST00000483040.1	n.79-19208C>T		intron_variant, non_coding_transcript_variant		5

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

Gnomad4 AFR AF: 0.536

Gnomad4 AMR AF: 0.765

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.778

Gnomad4 SAS AF: 0.905

Gnomad4 FIN AF: 0.823

Gnomad4 NFE AF: 0.852

Gnomad4 OTH AF: 0.780

Alfa AF: 0.779 Hom.: 7618

Bravo AF: 0.736

Asia WGS AF: 0.851 AC: 2957 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	0.41
DANN	Benign	0.53

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: rs1370868; hg19: chr10-132984356;