rs10829970

chr10-131309512-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_174937.4(TCERG1L):c.343-213G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0707 in 152,124 control chromosomes in the GnomAD database, including 472 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 0.071 (472 hom., cov: 32)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.637

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=-0.91).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.163 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCERG1L	NM_174937.4	c.343-213G>A		intron_variant		ENST00000368642.4
TCERG1L	XM_047424966.1	c.343-213G>A		intron_variant
TCERG1L	XM_047424967.1	c.343-213G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCERG1L	ENST00000368642.4	c.343-213G>A		intron_variant		1	NM_174937.4	P1

Frequencies

GnomAD3 genomes AF: 0.0708 AC: 10758 AN: 152008 Hom.: 473 Cov.: 32

Gnomad AFR AF: 0.0687

Gnomad AMI AF: 0.0241

Gnomad AMR AF: 0.0438

Gnomad ASJ AF: 0.0668

Gnomad EAS AF: 0.172

Gnomad SAS AF: 0.150

Gnomad FIN AF: 0.107

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0600

Gnomad OTH AF: 0.0695

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

GnomAD4 genome AF: 0.0707 AC: 10760 AN: 152124 Hom.: 472 Cov.: 32 AF XY: 0.0738 AC XY: 5484 AN XY: 74356

Gnomad4 AFR AF: 0.0686

Gnomad4 AMR AF: 0.0437

Gnomad4 ASJ AF: 0.0668

Gnomad4 EAS AF: 0.173

Gnomad4 SAS AF: 0.149

Gnomad4 FIN AF: 0.107

Gnomad4 NFE AF: 0.0600

Gnomad4 OTH AF: 0.0689

Alfa AF: 0.0635 Hom.: 427

Bravo AF: 0.0647

Asia WGS AF: 0.166 AC: 578 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.91
Cadd	Benign	0.14
Dann	Benign	0.68

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: rs10829970; hg19: chr10-133107775;