rs10765037

chr10-131134207-G-Achr10-131134207-G-C

Variant summary

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

The NM_174937.4(TCERG1L):c.1259+172C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.264 in 152,086 control chromosomes in the GnomAD database, including 5,507 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 0.26 (5507 hom., cov: 33)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.85

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=-0.94).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.377 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TCERG1L	NM_174937.4	c.1259+172C>T		intron_variant		ENST00000368642.4
TCERG1L	XM_047424966.1	c.1298+172C>T		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TCERG1L	ENST00000368642.4	c.1259+172C>T		intron_variant		1	NM_174937.4	P1
TCERG1L	ENST00000483040.1	n.3121+172C>T		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.264 AC: 40192 AN: 151966 Hom.: 5508 Cov.: 33

Gnomad AFR AF: 0.178

Gnomad AMI AF: 0.243

Gnomad AMR AF: 0.309

Gnomad ASJ AF: 0.275

Gnomad EAS AF: 0.297

Gnomad SAS AF: 0.392

Gnomad FIN AF: 0.321

Gnomad MID AF: 0.266

Gnomad NFE AF: 0.287

Gnomad OTH AF: 0.268

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

GnomAD4 genome AF: 0.264 AC: 40216 AN: 152086 Hom.: 5507 Cov.: 33 AF XY: 0.268 AC XY: 19884 AN XY: 74328

Gnomad4 AFR AF: 0.178

Gnomad4 AMR AF: 0.310

Gnomad4 ASJ AF: 0.275

Gnomad4 EAS AF: 0.296

Gnomad4 SAS AF: 0.392

Gnomad4 FIN AF: 0.321

Gnomad4 NFE AF: 0.287

Gnomad4 OTH AF: 0.266

Alfa AF: 0.166 Hom.: 354

Bravo AF: 0.257

Asia WGS AF: 0.355 AC: 1233 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
Cadd	Benign	0.31
Dann	Benign	0.51

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: rs10765037; hg19: chr10-132932470;