Genetic Variant TCP10L3:n.1045C>T (chr6-167373273-G-A) – ACMG Classification: Uncertain_significance (2 pts)

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PP3_Moderate

The ENST00000397829.8(TCP10L3):n.1045C>T 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 0.0034 in 150,816 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as not provided (no stars).

Frequency

Genomes: 𝑓 0.0034 ( 0 hom., cov: 41)

Exomes 𝑓: 0.00045 ( 1 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: 0.0440

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 Uncertain_significance. Variant got 2 ACMG points.

PP3

BayesDel_addAF computational evidence supports a deleterious effect, 0.262

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TCP10L3	NR_163193.1 link	n.943C>T	non_coding_transcript_exon_variant	Exon 6 of 6
TCP10L3	NR_163194.1 link	n.1089C>T	non_coding_transcript_exon_variant	Exon 8 of 8
TCP10L3	NR_163195.1 link	n.1016C>T	non_coding_transcript_exon_variant	Exon 7 of 7
TCP10L3	NR_163196.1 link	n.728C>T	non_coding_transcript_exon_variant	Exon 6 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TCP10L3	ENST00000397829.8 link	n.1045C>T	non_coding_transcript_exon_variant	Exon 8 of 8	1
TCP10L3	ENST00000514083.1 link	n.1539C>T	non_coding_transcript_exon_variant	Exon 2 of 2	1
TCP10L3	ENST00000463894.7 link	n.3324C>T	non_coding_transcript_exon_variant	Exon 6 of 6	2

Frequencies

GnomAD3 genomes

AF:

0.00340

AC:

513

AN:

150698

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00418

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00278

Gnomad ASJ

AF:

0.00321

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.000621

Gnomad FIN

AF:

0.00227

Gnomad MID

AF:

0.00318

Gnomad NFE

AF:

0.00366

Gnomad OTH

AF:

0.00674

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000449

AC:

651

AN:

1450478

Hom.:

Cov.:

AF XY:

0.000461

AC XY:

333

AN XY:

721610

show subpopulations

Gnomad4 AFR exome

AF:

0.00500

Gnomad4 AMR exome

AF:

0.000338

Gnomad4 ASJ exome

AF:

0.000618

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.0000697

Gnomad4 FIN exome

AF:

0.000453

Gnomad4 NFE exome

AF:

0.000336

Gnomad4 OTH exome

AF:

0.000818

GnomAD4 genome

AF:

0.00340

AC:

513

AN:

150816

Hom.:

Cov.:

AF XY:

0.00350

AC XY:

258

AN XY:

73806

show subpopulations

Gnomad4 AFR

AF:

0.00415

Gnomad4 AMR

AF:

0.00277

Gnomad4 ASJ

AF:

0.00321

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.000829

Gnomad4 FIN

AF:

0.00227

Gnomad4 NFE

AF:

0.00366

Gnomad4 OTH

AF:

0.00667

Alfa

AF:

0.00360

Hom.:

ESP6500AA

AF:

0.00347

AC:

ESP6500EA

AF:

0.00

AC:

ExAC

AF:

0.00222

AC:

268

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

Pathogenic

0.26

BayesDel_noAF

Pathogenic

0.14

CADD

Benign

7.7

DANN

Benign

0.93

Eigen

Benign

-0.30

Eigen_PC

Benign

-0.70

FATHMM_MKL

Benign

0.051

Vest4

0.049

GERP RS

0.93

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