Variant chr10-131185558-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.497

Variant links:

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 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

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 linkuse as main transcript	c.857-18673G>A		intron_variant		ENST00000368642.4	NP_777597.2
TCERG1L	XM_047424966.1 linkuse as main transcript	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 linkuse as main transcript	c.857-18673G>A		intron_variant		1	NM_174937.4	ENSP00000357631	P1
TCERG1L	ENST00000483040.1 linkuse as main transcript	n.79-18673G>A		intron_variant, non_coding_transcript_variant		5

Frequencies

GnomAD3 genomes

AF:

0.333

AC:

50601

AN:

151812

Hom.:

9659

Cov.:

show subpopulations

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.:

AF XY:

0.331

AC XY:

24586

AN XY:

74246

show subpopulations

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Computational scores

Splicing

Publications

LitVar

Other links and lift over