rs2397752

Positions:

• chr10-131185558-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.857-18673G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.334 in 151,932 control chromosomes in the GnomAD database, including 9,692 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 0.33 (9692 hom., cov: 32)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.497

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 (AFR) allele frequency at 95% confidence interval = 0.525 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCERG1L	NM_174937.4	c.857-18673G>A		intron_variant		ENST00000368642.4	NP_777597.2
TCERG1L	XM_047424966.1	c.857-18673G>A		intron_variant			XP_047280922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCERG1L	ENST00000368642.4	c.857-18673G>A		intron_variant		1	NM_174937.4	ENSP00000357631	P1
TCERG1L	ENST00000483040.1	n.79-18673G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes AF: 0.333 AC: 50601 AN: 151812 Hom.: 9659 Cov.: 32

Gnomad AFR AF: 0.530

Gnomad AMI AF: 0.128

Gnomad AMR AF: 0.304

Gnomad ASJ AF: 0.221

Gnomad EAS AF: 0.254

Gnomad SAS AF: 0.292

Gnomad FIN AF: 0.271

Gnomad MID AF: 0.342

Gnomad NFE AF: 0.247

Gnomad OTH AF: 0.326

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

GnomAD4 genome AF: 0.334 AC: 50688 AN: 151932 Hom.: 9692 Cov.: 32 AF XY: 0.331 AC XY: 24586 AN XY: 74246

Gnomad4 AFR AF: 0.531

Gnomad4 AMR AF: 0.304

Gnomad4 ASJ AF: 0.221

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.292

Gnomad4 FIN AF: 0.271

Gnomad4 NFE AF: 0.247

Gnomad4 OTH AF: 0.328

Alfa AF: 0.269 Hom.: 5903

Bravo AF: 0.347

Asia WGS AF: 0.297 AC: 1035 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	1.9
DANN	Benign	0.55

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: rs2397752; hg19: chr10-132983821; COSMIC: COSV64046243;