Variant 6-167376565-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The NR_163196.1(TCP10L3):n.408G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).

Frequency

Genomes: 𝑓 0.011 ( 4 hom., cov: 4)

Exomes 𝑓: 0.052 ( 19506 hom. )

Failed GnomAD Quality Control

Consequence

TCP10L3
NR_163196.1 non_coding_transcript_exon

Scores

Clinical Significance

Benign criteria provided, single submitter B:1

Conservation

PhyloP100: -0.396

Variant links:

Genes affected

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 Likely_benign. Variant got -6 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.004590988).

BP6

Variant 6-167376565-C-T is Benign according to our data. Variant chr6-167376565-C-T is described in ClinVar as [Benign]. Clinvar id is 768121.Status of the report is criteria_provided_single_submitter, 1 stars.

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	#exon/exons
TCP10L3	NR_163196.1 linkuse as main transcript	n.408G>A	non_coding_transcript_exon_variant	3/6
TCP10L3	NR_163193.1 linkuse as main transcript	n.623G>A	non_coding_transcript_exon_variant	3/6
TCP10L3	NR_163194.1 linkuse as main transcript	n.769G>A	non_coding_transcript_exon_variant	5/8
TCP10L3	NR_163195.1 linkuse as main transcript	n.696G>A	non_coding_transcript_exon_variant	4/7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TCP10L3	ENST00000366827.6 linkuse as main transcript	n.769G>A		non_coding_transcript_exon_variant	5/9	5
TCP10L3	ENST00000675664.1 linkuse as main transcript	n.638G>A		non_coding_transcript_exon_variant	4/9

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

616

AN:

57512

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.0147

Gnomad AMI

AF:

0.00340

Gnomad AMR

AF:

0.0122

Gnomad ASJ

AF:

0.0199

Gnomad EAS

AF:

0.0169

Gnomad SAS

AF:

0.0148

Gnomad FIN

AF:

0.00187

Gnomad MID

AF:

0.0268

Gnomad NFE

AF:

0.00826

Gnomad OTH

AF:

0.0183

GnomAD3 exomes

AF:

0.0788

AC:

10343

AN:

131330

Hom.:

5082

AF XY:

0.0792

AC XY:

5613

AN XY:

70834

show subpopulations

Gnomad AFR exome

AF:

0.0870

Gnomad AMR exome

AF:

0.139

Gnomad ASJ exome

AF:

0.0505

Gnomad EAS exome

AF:

0.164

Gnomad SAS exome

AF:

0.158

Gnomad FIN exome

AF:

0.0107

Gnomad NFE exome

AF:

0.0472

Gnomad OTH exome

AF:

0.102

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0522

AC:

40408

AN:

774670

Hom.:

19506

Cov.:

AF XY:

0.0573

AC XY:

22006

AN XY:

383944

show subpopulations

Gnomad4 AFR exome

AF:

0.0462

Gnomad4 AMR exome

AF:

0.119

Gnomad4 ASJ exome

AF:

0.0857

Gnomad4 EAS exome

AF:

0.0822

Gnomad4 SAS exome

AF:

0.211

Gnomad4 FIN exome

AF:

0.0604

Gnomad4 NFE exome

AF:

0.0376

Gnomad4 OTH exome

AF:

0.0579

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.0107

AC:

615

AN:

57576

Hom.:

Cov.:

AF XY:

0.00991

AC XY:

278

AN XY:

28050

show subpopulations

Gnomad4 AFR

AF:

0.0147

Gnomad4 AMR

AF:

0.0120

Gnomad4 ASJ

AF:

0.0199

Gnomad4 EAS

AF:

0.0169

Gnomad4 SAS

AF:

0.0147

Gnomad4 FIN

AF:

0.00187

Gnomad4 NFE

AF:

0.00826

Gnomad4 OTH

AF:

0.0182

Alfa

AF:

0.0909

Hom.:

219

ExAC

AF:

0.0000963

AC:

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

Dec 31, 2019

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.39

BayesDel_noAF

Benign

-0.80

CADD

Benign

3.9

DANN

Benign

0.37

Eigen

Benign

-1.6

Eigen_PC

Benign

-1.7

FATHMM_MKL

Benign

0.0062

LIST_S2

Benign

0.41

.;T;T

M_CAP

Benign

0.0011

MetaRNN

Benign

0.0046

T;T;T

MetaSVM

Benign

-0.98

MutationTaster

Benign

1.0

P;P

PrimateAI

Benign

0.35

PROVEAN

Benign

1.5

N;N;.

REVEL

Benign

0.054

Sift

Benign

0.58

T;T;.

Sift4G

Benign

0.45

T;T;T

Polyphen

0.69

.;P;.

Vest4

0.080

MPC

2.2

ClinPred

0.0074

GERP RS

-3.3

gMVP

0.040

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