Variant rs2345794 details in Genebe, Genetics Data Aggregator

Variant summary

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

The ENST00000397829.8(TCP10L3):n.725G>C 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. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: 𝑓 0.0 ( 0 hom., cov: 4)

Exomes 𝑓: 0.0 ( 0 hom. )

Failed GnomAD Quality Control

Consequence

TCP10L3
ENST00000397829.8 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.396

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=0.05909109).

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TCP10L3	NR_163193.1 link	n.623G>C	non_coding_transcript_exon_variant	Exon 3 of 6
TCP10L3	NR_163194.1 link	n.769G>C	non_coding_transcript_exon_variant	Exon 5 of 8
TCP10L3	NR_163195.1 link	n.696G>C	non_coding_transcript_exon_variant	Exon 4 of 7
TCP10L3	NR_163196.1 link	n.408G>C	non_coding_transcript_exon_variant	Exon 3 of 6

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TCP10L3	ENST00000397829.8 link	n.725G>C	non_coding_transcript_exon_variant	Exon 5 of 8	1
TCP10L3	ENST00000460930.2 link	n.545G>C	non_coding_transcript_exon_variant	Exon 3 of 3	1
TCP10L3	ENST00000366827.6 link	n.769G>C	non_coding_transcript_exon_variant	Exon 5 of 9	5

Frequencies

GnomAD3 genomes

AF:

0.00

AC:

AN:

59388

Hom.:

Cov.:

FAILED QC

Gnomad AFR

AF:

0.00

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00

Gnomad OTH

AF:

0.00

GnomAD4 exome

Data not reliable, filtered out with message: AC0

AF:

0.00

AC:

AN:

789066

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

391038

Gnomad4 AFR exome

AF:

0.00

Gnomad4 AMR exome

AF:

0.00

Gnomad4 ASJ exome

AF:

0.00

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.00

Gnomad4 FIN exome

AF:

0.00

Gnomad4 NFE exome

AF:

0.00

Gnomad4 OTH exome

AF:

0.00

GnomAD4 genome

Data not reliable, filtered out with message: AC0;AS_VQSR

AF:

0.00

AC:

AN:

59388

Hom.:

Cov.:

AF XY:

0.00

AC XY:

AN XY:

28766

Gnomad4 AFR

AF:

0.00

Gnomad4 AMR

AF:

0.00

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00

Gnomad4 FIN

AF:

0.00

Gnomad4 NFE

AF:

0.00

Gnomad4 OTH

AF:

0.00

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_addAF

Benign

-0.37

BayesDel_noAF

Benign

-0.78

CADD

Benign

3.2

DANN

Benign

0.075

Eigen

Benign

-1.5

Eigen_PC

Benign

-1.6

FATHMM_MKL

Benign

0.010

LIST_S2

Benign

0.52

.;T;T

M_CAP

Benign

0.0012

MetaRNN

Benign

0.059

T;T;T

MetaSVM

Benign

-1.0

PrimateAI

Benign

0.34

PROVEAN

Benign

0.24

N;N;.

REVEL

Benign

0.037

Sift

Benign

1.0

T;T;.

Sift4G

Benign

0.18

T;T;T

Polyphen

0.018

.;B;.

Vest4

0.11

MVP

0.014

MPC

2.2

ClinPred

0.035

GERP RS

-3.3

gMVP

0.050

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