chr10-131170839-A-G

Variant names:

• chr10-131170839-A-G
• rs2008589
• NM_174937.4:c.857-3954T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_174937.4(TCERG1L):​c.857-3954T>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
• Publications: 1 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=-0.94).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.868 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_174937.4. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	NM_174937.4	MANE Select	c.857-3954T>C		intron	N/A	NP_777597.2

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCERG1L	ENST00000368642.4	TSL:1 MANE Select	c.857-3954T>C		intron	N/A	ENSP00000357631.4
	TCERG1L	ENST00000483040.1	TSL:5	n.79-3954T>C		intron	N/A

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

African (AFR) AF: 0.691 AC: 28576 AN: 41378

American (AMR) AF: 0.757 AC: 11540 AN: 15248

Ashkenazi Jewish (ASJ) AF: 0.867 AC: 3005 AN: 3466

East Asian (EAS) AF: 0.688 AC: 3511 AN: 5104

South Asian (SAS) AF: 0.855 AC: 4114 AN: 4814

European-Finnish (FIN) AF: 0.870 AC: 9152 AN: 10516

Middle Eastern (MID) AF: 0.861 AC: 253 AN: 294

European-Non Finnish (NFE) AF: 0.874 AC: 59325 AN: 67888

Other (OTH) AF: 0.806 AC: 1702 AN: 2112

Alfa AF: 0.832 Hom.: 6871

Bravo AF: 0.788

Asia WGS AF: 0.760 AC: 2639 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.87
DANN	Benign	0.29
PhyloP100		-0.010
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: rs2008589; hg19: chr10-132969102;