Variant chr6-167376622-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1

The ENST00000397829.8(TCP10L3):n.668G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0401 in 829,432 control chromosomes in the GnomAD database, including 189 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.016 ( 5 hom., cov: 8)

Exomes 𝑓: 0.040 ( 189 hom. )

Failed GnomAD Quality Control

Consequence

TCP10L3
ENST00000397829.8 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.0490

Variant links:

Genes affected

TCP10L3 (HGNC:):

TCP10L3 links:

TCP10L3 (HGNC:11656): (t-complex 10 like 3 (pseudogene))

TCP10L3 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -14 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004687518).

BP6

Variant 6-167376622-C-T is Benign according to our data. Variant chr6-167376622-C-T is described in ClinVar as [Benign]. Clinvar id is 768122.Status of the report is criteria_provided_single_submitter, 1 stars.

BA1

GnomAdExome4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.0991 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
TCP10L3	NR_163193.1 link	n.566G>A	non_coding_transcript_exon_variant	3/6
TCP10L3	NR_163194.1 link	n.712G>A	non_coding_transcript_exon_variant	5/8
TCP10L3	NR_163195.1 link	n.639G>A	non_coding_transcript_exon_variant	4/7
TCP10L3	NR_163196.1 link	n.351G>A	non_coding_transcript_exon_variant	3/6

Ensembl

Gene	Transcript	HGVSc	Effect	#exon/exons	TSL
TCP10L3	ENST00000397829.8 link	n.668G>A	non_coding_transcript_exon_variant	5/8	1
TCP10L3	ENST00000460930.2 link	n.488G>A	non_coding_transcript_exon_variant	3/3	1
TCP10L3	ENST00000366827.6 link	n.712G>A	non_coding_transcript_exon_variant	5/9	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

1075

AN:

65752

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00662

Gnomad AMI

AF:

0.00811

Gnomad AMR

AF:

0.0167

Gnomad ASJ

AF:

0.0196

Gnomad EAS

AF:

0.0245

Gnomad SAS

AF:

0.0388

Gnomad FIN

AF:

0.00721

Gnomad MID

AF:

0.0313

Gnomad NFE

AF:

0.0220

Gnomad OTH

AF:

0.0188

GnomAD3 exomes

AF:

0.0297

AC:

4063

AN:

136628

Hom.:

AF XY:

0.0292

AC XY:

2142

AN XY:

73450

show subpopulations

Gnomad AFR exome

AF:

0.0132

Gnomad AMR exome

AF:

0.0366

Gnomad ASJ exome

AF:

0.0267

Gnomad EAS exome

AF:

0.0581

Gnomad SAS exome

AF:

0.0433

Gnomad FIN exome

AF:

0.00433

Gnomad NFE exome

AF:

0.0272

Gnomad OTH exome

AF:

0.0427

GnomAD4 exome

AF:

0.0401

AC:

33270

AN:

829432

Hom.:

189

Cov.:

AF XY:

0.0429

AC XY:

17831

AN XY:

415268

show subpopulations

Gnomad4 AFR exome

AF:

0.0150

Gnomad4 AMR exome

AF:

0.0522

Gnomad4 ASJ exome

AF:

0.0647

Gnomad4 EAS exome

AF:

0.0641

Gnomad4 SAS exome

AF:

0.101

Gnomad4 FIN exome

AF:

0.0451

Gnomad4 NFE exome

AF:

0.0333

Gnomad4 OTH exome

AF:

0.0488

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0163

AC:

1075

AN:

65812

Hom.:

Cov.:

AF XY:

0.0143

AC XY:

451

AN XY:

31498

show subpopulations

Gnomad4 AFR

AF:

0.00665

Gnomad4 AMR

AF:

0.0165

Gnomad4 ASJ

AF:

0.0196

Gnomad4 EAS

AF:

0.0250

Gnomad4 SAS

AF:

0.0397

Gnomad4 FIN

AF:

0.00721

Gnomad4 NFE

AF:

0.0220

Gnomad4 OTH

AF:

0.0187

Alfa

AF:

0.0991

Hom.:

ExAC

AF:

0.00156

AC:

103

ClinVar

Significance: Benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Benign, criteria provided, single submitter

clinical testing

Labcorp Genetics (formerly Invitae), Labcorp

Mar 05, 2018

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.71

BayesDel_noAF

Benign

-0.76

CADD

Benign

4.4

DANN

Benign

0.91

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0026

LIST_S2

Benign

0.48

.;T;T

M_CAP

Benign

0.0023

MetaRNN

Benign

0.0047

T;T;T

MetaSVM

Benign

-0.99

PrimateAI

Benign

0.34

PROVEAN

Benign

-0.36

N;N;.

REVEL

Benign

0.060

Sift

Benign

0.48

T;T;.

Sift4G

Benign

0.30

T;T;T

Polyphen

0.0

.;B;.

Vest4

0.043

MPC

2.1

ClinPred

0.0012

GERP RS

-3.8

gMVP

0.059

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

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over