Genetic Variant TCP10L3:n.1120G>A (chr6-167373198-C-T) – ACMG Classification: Likely_benign (-4 pts)

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000397829.8(TCP10L3):n.1120G>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 0.00419 in 151,778 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.0042 ( 0 hom., cov: 41)

Exomes 𝑓: 0.0057 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TCP10L3
ENST00000397829.8 non_coding_transcript_exon

Scores

Clinical Significance

not provided no classification provided O:1

Conservation

PhyloP100: -0.913

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 Likely_benign. Variant got -4 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.006129205).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TCP10L3	NR_163193.1 link	n.1018G>A	non_coding_transcript_exon_variant	Exon 6 of 6
TCP10L3	NR_163194.1 link	n.1164G>A	non_coding_transcript_exon_variant	Exon 8 of 8
TCP10L3	NR_163195.1 link	n.1091G>A	non_coding_transcript_exon_variant	Exon 7 of 7
TCP10L3	NR_163196.1 link	n.803G>A	non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TCP10L3	ENST00000397829.8 link	n.1120G>A	non_coding_transcript_exon_variant	Exon 8 of 8	1
TCP10L3	ENST00000514083.1 link	n.1614G>A	non_coding_transcript_exon_variant	Exon 2 of 2	1
TCP10L3	ENST00000463894.7 link	n.3399G>A	non_coding_transcript_exon_variant	Exon 6 of 6	2

Frequencies

GnomAD3 genomes

AF:

0.00421

AC:

638

AN:

151660

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.000942

Gnomad AMI

AF:

0.00110

Gnomad AMR

AF:

0.00546

Gnomad ASJ

AF:

0.000864

Gnomad EAS

AF:

0.00445

Gnomad SAS

AF:

0.00104

Gnomad FIN

AF:

0.00435

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00622

Gnomad OTH

AF:

0.00815

GnomAD3 exomes

AF:

0.00460

AC:

1140

AN:

247960

Hom.:

AF XY:

0.00451

AC XY:

607

AN XY:

134532

show subpopulations

Gnomad AFR exome

AF:

0.000712

Gnomad AMR exome

AF:

0.00492

Gnomad ASJ exome

AF:

0.00110

Gnomad EAS exome

AF:

0.00195

Gnomad SAS exome

AF:

0.00196

Gnomad FIN exome

AF:

0.00666

Gnomad NFE exome

AF:

0.00610

Gnomad OTH exome

AF:

0.00433

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00570

AC:

8279

AN:

1451496

Hom.:

Cov.:

AF XY:

0.00551

AC XY:

3977

AN XY:

722042

show subpopulations

Gnomad4 AFR exome

AF:

0.000598

Gnomad4 AMR exome

AF:

0.00455

Gnomad4 ASJ exome

AF:

0.00165

Gnomad4 EAS exome

AF:

0.00345

Gnomad4 SAS exome

AF:

0.00145

Gnomad4 FIN exome

AF:

0.00633

Gnomad4 NFE exome

AF:

0.00644

Gnomad4 OTH exome

AF:

0.00497

GnomAD4 genome

AF:

0.00419

AC:

636

AN:

151778

Hom.:

Cov.:

AF XY:

0.00399

AC XY:

296

AN XY:

74226

show subpopulations

Gnomad4 AFR

AF:

0.000939

Gnomad4 AMR

AF:

0.00539

Gnomad4 ASJ

AF:

0.000864

Gnomad4 EAS

AF:

0.00426

Gnomad4 SAS

AF:

0.00104

Gnomad4 FIN

AF:

0.00435

Gnomad4 NFE

AF:

0.00622

Gnomad4 OTH

AF:

0.00806

Alfa

AF:

0.00546

Hom.:

ESP6500AA

AF:

0.00135

AC:

ESP6500EA

AF:

0.00549

AC:

ExAC

AF:

0.00697

AC:

842

EpiCase

AF:

0.00347

EpiControl

AF:

0.00489

ClinVar

Significance: not provided

Submissions summary: Other:1

Revision: no classification provided

LINK: link

Submissions by phenotype

not provided

Other:1

GenomeConnect, ClinGen

Significance: not provided

Review Status: no classification provided

Collection Method: phenotyping only

GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant. -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.64

BayesDel_noAF

Benign

-0.68

CADD

Benign

0.41

DANN

Uncertain

0.99

Eigen

Benign

-1.1

Eigen_PC

Benign

-1.3

FATHMM_MKL

Benign

0.030

LIST_S2

Benign

0.38

T;T;T

M_CAP

Benign

0.0016

MetaRNN

Benign

0.0061

T;T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.32

PROVEAN

Benign

-0.25

N;.;.

REVEL

Benign

0.037

Sift

Pathogenic

0.0

D;.;.

Sift4G

Pathogenic

0.0

D;D;.

Vest4

0.045

MVP

0.11

MPC

0.82

ClinPred

0.046

GERP RS

-3.3

gMVP

0.037

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