Genetic Variant TCP10L2:n.818G>A (chr6-167180681-G-A) – ACMG Classification: Benign (-10 pts)

Variant summary

Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP4_StrongBP6_ModerateBS2

The ENST00000697192.1(TCP10L2):n.818G>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 Likely benign (★).

Frequency

Genomes: 𝑓 0.0033 ( 8 hom., cov: 9)

Exomes 𝑓: 0.0030 ( 86 hom. )

Failed GnomAD Quality Control

Consequence

TCP10L2
ENST00000697192.1 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: -3.52

Variant links:

Genes affected

TCP10L2 (HGNC:21254): (t-complex 10 like 2 (pseudogene))

TCP10L2 links:

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -10 ACMG points.

BP4

Computational evidence support a benign effect (MetaRNN=0.00506106).

BP6

Variant 6-167180681-G-A is Benign according to our data. Variant chr6-167180681-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 2657127.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 86 AR gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect	Exon rank
TCP10L2	XR_001743415.1 link	n.1015G>A	non_coding_transcript_exon_variant	Exon 7 of 10
TCP10L2	XR_007059868.1 link	n.923G>A	non_coding_transcript_exon_variant	Exon 7 of 10
TCP10L2	XR_007059869.1 link	n.923G>A	non_coding_transcript_exon_variant	Exon 7 of 11

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TCP10L2	ENST00000697192.1 link	n.818G>A		non_coding_transcript_exon_variant	Exon 6 of 10

Frequencies

GnomAD3 genomes

AF:

0.00327

AC:

238

AN:

72678

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.00176

Gnomad AMI

AF:

0.0234

Gnomad AMR

AF:

0.000538

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00161

Gnomad FIN

AF:

0.00534

Gnomad MID

AF:

0.00

Gnomad NFE

AF:

0.00438

Gnomad OTH

AF:

0.00113

GnomAD3 exomes

AF:

0.00180

AC:

100

AN:

55486

Hom.:

AF XY:

0.00189

AC XY:

AN XY:

28052

show subpopulations

Gnomad AFR exome

AF:

0.000606

Gnomad AMR exome

AF:

0.000770

Gnomad ASJ exome

AF:

0.00

Gnomad EAS exome

AF:

0.00

Gnomad SAS exome

AF:

0.000185

Gnomad FIN exome

AF:

0.00431

Gnomad NFE exome

AF:

0.00286

Gnomad OTH exome

AF:

0.000581

GnomAD4 exome

AF:

0.00298

AC:

1861

AN:

624438

Hom.:

Cov.:

AF XY:

0.00285

AC XY:

899

AN XY:

315850

show subpopulations

Gnomad4 AFR exome

AF:

0.000556

Gnomad4 AMR exome

AF:

0.000603

Gnomad4 ASJ exome

AF:

0.0000702

Gnomad4 EAS exome

AF:

0.00

Gnomad4 SAS exome

AF:

0.000682

Gnomad4 FIN exome

AF:

0.00448

Gnomad4 NFE exome

AF:

0.00351

Gnomad4 OTH exome

AF:

0.00306

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.00327

AC:

238

AN:

72696

Hom.:

Cov.:

AF XY:

0.00307

AC XY:

103

AN XY:

33554

show subpopulations

Gnomad4 AFR

AF:

0.00175

Gnomad4 AMR

AF:

0.000538

Gnomad4 ASJ

AF:

0.00

Gnomad4 EAS

AF:

0.00

Gnomad4 SAS

AF:

0.00161

Gnomad4 FIN

AF:

0.00534

Gnomad4 NFE

AF:

0.00438

Gnomad4 OTH

AF:

0.00113

Alfa

AF:

0.00313

Hom.:

ExAC

AF:

0.000596

AC:

ClinVar

Significance: Likely benign

Submissions summary: Benign:1

Revision: criteria provided, single submitter

LINK: link

Submissions by phenotype

not provided

Benign:1

Jan 01, 2023

CeGaT Center for Human Genetics Tuebingen

Significance: Likely benign

Review Status: criteria provided, single submitter

Collection Method: clinical testing

TCP10L2: PP2, BP4, BS2 -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.085

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.088

DANN

Benign

0.39

DEOGEN2

Benign

0.00051

Eigen

Benign

-2.0

Eigen_PC

Benign

-2.1

FATHMM_MKL

Benign

0.00031

LIST_S2

Benign

0.48

M_CAP

Benign

0.00089

MetaRNN

Benign

0.0051

MetaSVM

Benign

-0.97

MutationAssessor

Benign

-1.5

PrimateAI

Benign

0.29

PROVEAN

Benign

1.3

REVEL

Benign

0.0070

Sift

Benign

1.0

Sift4G

Benign

0.95

Polyphen

0.0

Vest4

0.033

MVP

0.043

MPC

1.8

ClinPred

0.0024

GERP RS

-2.6

Varity_R

0.018

gMVP

0.044

Splicing

Name

Calibrated prediction

Score

Prediction

SpliceAI score (max)

0.010

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