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

Variant summary

Our verdict is Benign. The variant received -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

Publications

3 publications found

Variant links:

Genes affected

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

TCP10L2 links:

ENSG00000286674 (HGNC:):

ENSG00000286674 links:

Genome browser will be placed here

new If you want to explore the variant's impact on the transcript ENST00000697192.1, check out the Mutation Effect Viewer. This is especially useful for frameshift variants or if you want to visualize the effect of exon loss / intron retention.

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -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 VariationId is 2657127.Status of the report is criteria_provided_single_submitter, 1 stars.

BS2

High Homozygotes in GnomAdExome4 at 86 AR gene

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000697192.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TCP10L2	ENST00000697192.1		n.818G>A		non_coding_transcript_exon	Exon 6 of 10
	ENSG00000286674	ENST00000810162.1		n.439-14258C>T		intron	N/A

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

GnomAD2 exomes

AF:

0.00180

AC:

100

AN:

55486

AF XY:

0.00189

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 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

African (AFR)

AF:

0.000556

AC:

AN:

14398

American (AMR)

AF:

0.000603

AC:

AN:

14936

Ashkenazi Jewish (ASJ)

AF:

0.0000702

AC:

AN:

14242

East Asian (EAS)

AF:

0.00

AC:

AN:

21680

South Asian (SAS)

AF:

0.000682

AC:

AN:

46926

European-Finnish (FIN)

AF:

0.00448

AC:

150

AN:

33446

Middle Eastern (MID)

AF:

0.000463

AC:

AN:

2158

European-Non Finnish (NFE)

AF:

0.00351

AC:

1574

AN:

448522

Other (OTH)

AF:

0.00306

AC:

AN:

28130

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.431

Heterozygous variant carriers

112

168

224

280

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

126

168

210

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

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

African (AFR)

AF:

0.00175

AC:

AN:

17102

American (AMR)

AF:

0.000538

AC:

AN:

5576

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

2196

East Asian (EAS)

AF:

0.00

AC:

AN:

2570

South Asian (SAS)

AF:

0.00161

AC:

AN:

1864

European-Finnish (FIN)

AF:

0.00534

AC:

AN:

4680

Middle Eastern (MID)

AF:

0.00

AC:

AN:

210

European-Non Finnish (NFE)

AF:

0.00438

AC:

162

AN:

37016

Other (OTH)

AF:

0.00113

AC:

AN:

884

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.467

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

<30

30-35

35-40

40-45

45-50

50-55

55-60

60-65

65-70

70-75

75-80

>80

Age

Alfa

AF:

0.00313

Hom.:

ClinVar

ClinVar submissions

Significance:Likely benign

Revision:criteria provided, single submitter

View on ClinVar

Pathogenic

VUS

Benign

Condition

not provided (1)

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

AlphaMissense

Benign

0.085

BayesDel_addAF

Benign

-0.74

BayesDel_noAF

Benign

-0.84

CADD

Benign

0.088

(source)

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

PhyloP100

-3.5

PrimateAI

Benign

0.29

PROVEAN

Benign

1.3

REVEL

Benign

0.0070

Sift

Benign

1.0

Sift4G

Benign

0.95

Varity_R

0.018

gMVP

0.044

Mutation Taster

=100/0

polymorphism

(source)

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over