10-131123026-T-C

Variant names:

• chr10-131123026-T-C
• rs11017736
• NM_174937.4:c.1260-6092A>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.1260-6092A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.665 in 152,144 control chromosomes in the GnomAD database, including 34,169 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 0.67 (34169 hom., cov: 34)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -2.45
• Publications: 0 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=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.969 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCERG1L	NM_174937.4	c.1260-6092A>G		intron_variant	Intron 8 of 11	ENST00000368642.4	NP_777597.2
TCERG1L	XM_047424966.1	c.1299-6092A>G		intron_variant	Intron 9 of 12		XP_047280922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCERG1L	ENST00000368642.4	c.1260-6092A>G		intron_variant	Intron 8 of 11	1	NM_174937.4	ENSP00000357631.4
TCERG1L	ENST00000483040.1	n.3122-6092A>G		intron_variant	Intron 8 of 11	5

Frequencies

GnomAD3 genomes AF: 0.665 AC: 101113 AN: 152026 Hom.: 34131 Cov.: 34

Gnomad AFR AF: 0.612

Gnomad AMI AF: 0.707

Gnomad AMR AF: 0.741

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.991

Gnomad SAS AF: 0.797

Gnomad FIN AF: 0.677

Gnomad MID AF: 0.666

Gnomad NFE AF: 0.642

Gnomad OTH AF: 0.669

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

GnomAD4 genome AF: 0.665 AC: 101206 AN: 152144 Hom.: 34169 Cov.: 34 AF XY: 0.671 AC XY: 49938 AN XY: 74398

African (AFR) AF: 0.612 AC: 25401 AN: 41488

American (AMR) AF: 0.741 AC: 11342 AN: 15300

Ashkenazi Jewish (ASJ) AF: 0.693 AC: 2406 AN: 3470

East Asian (EAS) AF: 0.991 AC: 5103 AN: 5148

South Asian (SAS) AF: 0.798 AC: 3850 AN: 4826

European-Finnish (FIN) AF: 0.677 AC: 7183 AN: 10612

Middle Eastern (MID) AF: 0.661 AC: 193 AN: 292

European-Non Finnish (NFE) AF: 0.642 AC: 43661 AN: 67982

Other (OTH) AF: 0.673 AC: 1422 AN: 2114

Alfa AF: 0.660 Hom.: 17466

Bravo AF: 0.670

Asia WGS AF: 0.890 AC: 3093 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	0.032
DANN	Benign	0.38
PhyloP100		-2.4
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: rs11017736; hg19: chr10-132921289;