rs10829970

Variant names:

• chr10-131309512-C-T
• rs10829970
• NM_174937.4:c.343-213G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 4 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=-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 rank	MANE	Protein	UniProt
TCERG1L	NM_174937.4	c.343-213G>A		intron_variant	Intron 1 of 11	ENST00000368642.4	NP_777597.2
TCERG1L	XM_047424966.1	c.343-213G>A		intron_variant	Intron 1 of 12		XP_047280922.1
TCERG1L	XM_047424967.1	c.343-213G>A		intron_variant	Intron 1 of 4		XP_047280923.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCERG1L	ENST00000368642.4	c.343-213G>A		intron_variant	Intron 1 of 11	1	NM_174937.4	ENSP00000357631.4

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

African (AFR) AF: 0.0686 AC: 2847 AN: 41490

American (AMR) AF: 0.0437 AC: 669 AN: 15292

Ashkenazi Jewish (ASJ) AF: 0.0668 AC: 232 AN: 3472

East Asian (EAS) AF: 0.173 AC: 893 AN: 5170

South Asian (SAS) AF: 0.149 AC: 718 AN: 4818

European-Finnish (FIN) AF: 0.107 AC: 1132 AN: 10560

Middle Eastern (MID) AF: 0.0680 AC: 20 AN: 294

European-Non Finnish (NFE) AF: 0.0600 AC: 4082 AN: 68010

Other (OTH) AF: 0.0689 AC: 145 AN: 2106

Alfa AF: 0.0648 Hom.: 598

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
PhyloP100		-0.64
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: rs10829970; hg19: chr10-133107775;