rs11593241

Variant names:

• chr10-131188383-T-C
• rs11593241
• NM_174937.4:c.857-21498A>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.857-21498A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.109 in 152,192 control chromosomes in the GnomAD database, including 1,216 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 0.11 (1216 hom., cov: 33)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.937
• 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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.211 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TCERG1L	NM_174937.4	c.857-21498A>G		intron_variant	Intron 4 of 11	ENST00000368642.4	NP_777597.2
TCERG1L	XM_047424966.1	c.857-21498A>G		intron_variant	Intron 4 of 12		XP_047280922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCERG1L	ENST00000368642.4	c.857-21498A>G		intron_variant	Intron 4 of 11	1	NM_174937.4	ENSP00000357631.4
TCERG1L	ENST00000483040.1	n.79-21498A>G		intron_variant	Intron 1 of 11	5

Frequencies

GnomAD3 genomes AF: 0.109 AC: 16524 AN: 152074 Hom.: 1217 Cov.: 33

Gnomad AFR AF: 0.0255

Gnomad AMI AF: 0.0813

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.0899

Gnomad EAS AF: 0.222

Gnomad SAS AF: 0.0877

Gnomad FIN AF: 0.172

Gnomad MID AF: 0.111

Gnomad NFE AF: 0.128

Gnomad OTH AF: 0.113

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

GnomAD4 genome AF: 0.109 AC: 16524 AN: 152192 Hom.: 1216 Cov.: 33 AF XY: 0.112 AC XY: 8352 AN XY: 74398

African (AFR) AF: 0.0255 AC: 1058 AN: 41536

American (AMR) AF: 0.176 AC: 2692 AN: 15284

Ashkenazi Jewish (ASJ) AF: 0.0899 AC: 312 AN: 3470

East Asian (EAS) AF: 0.222 AC: 1147 AN: 5168

South Asian (SAS) AF: 0.0868 AC: 418 AN: 4818

European-Finnish (FIN) AF: 0.172 AC: 1817 AN: 10584

Middle Eastern (MID) AF: 0.105 AC: 31 AN: 294

European-Non Finnish (NFE) AF: 0.128 AC: 8737 AN: 68012

Other (OTH) AF: 0.112 AC: 238 AN: 2116

Alfa AF: 0.122 Hom.: 1014

Bravo AF: 0.109

Asia WGS AF: 0.118 AC: 411 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	8.2
DANN	Benign	0.68
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: rs11593241; hg19: chr10-132986646;