10-131170839-A-G

Position:

• chr10-131170839-A-G

Variant summary

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

The NM_174937.4(TCERG1L):​c.857-3954T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.804 in 151,730 control chromosomes in the GnomAD database, including 49,614 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 0.80 (49614 hom., cov: 32)
• Consequence: TCERG1L NM_174937.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0100

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]

TCERG1L (HGNC:):

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 (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TCERG1L	NM_174937.4	c.857-3954T>C		intron_variant		ENST00000368642.4	NP_777597.2
TCERG1L	XM_047424966.1	c.857-3954T>C		intron_variant			XP_047280922.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCERG1L	ENST00000368642.4	c.857-3954T>C		intron_variant		1	NM_174937.4	ENSP00000357631.4
TCERG1L	ENST00000483040.1	n.79-3954T>C		intron_variant		5

Frequencies

GnomAD3 genomes AF: 0.805 AC: 122015 AN: 151618 Hom.: 49612 Cov.: 32

Gnomad AFR AF: 0.691

Gnomad AMI AF: 0.959

Gnomad AMR AF: 0.757

Gnomad ASJ AF: 0.867

Gnomad EAS AF: 0.689

Gnomad SAS AF: 0.855

Gnomad FIN AF: 0.870

Gnomad MID AF: 0.858

Gnomad NFE AF: 0.874

Gnomad OTH AF: 0.807

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

GnomAD4 genome AF: 0.804 AC: 122051 AN: 151730 Hom.: 49614 Cov.: 32 AF XY: 0.804 AC XY: 59635 AN XY: 74128

Gnomad4 AFR AF: 0.691

Gnomad4 AMR AF: 0.757

Gnomad4 ASJ AF: 0.867

Gnomad4 EAS AF: 0.688

Gnomad4 SAS AF: 0.855

Gnomad4 FIN AF: 0.870

Gnomad4 NFE AF: 0.874

Gnomad4 OTH AF: 0.806

Alfa AF: 0.838 Hom.: 6684

Bravo AF: 0.788

Asia WGS AF: 0.760 AC: 2639 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	0.87
DANN	Benign	0.29

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: rs2008589; hg19: chr10-132969102;