Genetic Variant TCP10L3:n.642A>G (chr6-167376666-T-C) – ACMG Classification: Likely_benign (-6 pts)

Variant summary

Our verdict is Likely benign. The variant received -6 ACMG points: 0P and 6B. BP4_StrongBP6_Moderate

The ENST00000397829.9(TCP10L3):n.642A>G 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 0.00033 ( 3 hom., cov: 9)

Exomes 𝑓: 0.00034 ( 41 hom. )

Failed GnomAD Quality Control

Consequence

TCP10L3
ENST00000397829.9 non_coding_transcript_exon

Scores

Clinical Significance

Likely benign criteria provided, single submitter B:1

Conservation

PhyloP100: 0.389

Publications

0 publications found

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 was made for transcript

Our verdict: Likely_benign. The variant received -6 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.97).

BP6

Variant 6-167376666-T-C is Benign according to our data. Variant chr6-167376666-T-C is described in ClinVar as Likely_benign. ClinVar VariationId is 2657131.Status of the report is criteria_provided_single_submitter, 1 stars.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000397829.9. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	HGVSc	Effect	Exon Rank
TCP10L3	NR_163193.1	n.522A>G	non_coding_transcript_exon	Exon 3 of 6
TCP10L3	NR_163194.1	n.668A>G	non_coding_transcript_exon	Exon 5 of 8
TCP10L3	NR_163195.1	n.595A>G	non_coding_transcript_exon	Exon 4 of 7

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank
TCP10L3	ENST00000397829.9	TSL:1	n.642A>G	non_coding_transcript_exon	Exon 5 of 8
TCP10L3	ENST00000460930.2	TSL:1	n.444A>G	non_coding_transcript_exon	Exon 3 of 3
TCP10L3	ENST00000366827.6	TSL:5	n.668A>G	non_coding_transcript_exon	Exon 5 of 9

Frequencies

GnomAD3 genomes

AF:

0.000343

AC:

AN:

75772

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0000500

Gnomad AMI

AF:

0.00

Gnomad AMR

AF:

0.00205

Gnomad ASJ

AF:

0.00

Gnomad EAS

AF:

0.00

Gnomad SAS

AF:

0.00119

Gnomad FIN

AF:

0.00

Gnomad MID

AF:

0.00510

Gnomad NFE

AF:

0.000189

Gnomad OTH

AF:

0.00208

GnomAD2 exomes

AF:

0.000629

AC:

AN:

98518

AF XY:

0.000724

show subpopulations

Gnomad AFR exome

AF:

0.00

Gnomad AMR exome

AF:

0.00122

Gnomad ASJ exome

AF:

0.00496

Gnomad EAS exome

AF:

0.000111

Gnomad FIN exome

AF:

0.00

Gnomad NFE exome

AF:

0.000393

Gnomad OTH exome

AF:

0.00145

GnomAD4 exome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000342

AC:

289

AN:

846158

Hom.:

Cov.:

AF XY:

0.000350

AC XY:

149

AN XY:

426288

show subpopulations

African (AFR)

AF:

0.000328

AC:

AN:

21324

American (AMR)

AF:

0.000943

AC:

AN:

22276

Ashkenazi Jewish (ASJ)

AF:

0.00195

AC:

AN:

15872

East Asian (EAS)

AF:

0.0000359

AC:

AN:

27854

South Asian (SAS)

AF:

0.000347

AC:

AN:

54778

European-Finnish (FIN)

AF:

0.00

AC:

AN:

33936

Middle Eastern (MID)

AF:

0.00760

AC:

AN:

3420

European-Non Finnish (NFE)

AF:

0.000257

AC:

162

AN:

629328

Other (OTH)

AF:

0.000589

AC:

AN:

37370

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.604

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome 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

GnomAD4 genome

Data not reliable, filtered out with message: AS_VQSR

AF:

0.000330

AC:

AN:

75818

Hom.:

Cov.:

AF XY:

0.000309

AC XY:

AN XY:

35556

show subpopulations

African (AFR)

AF:

0.0000498

AC:

AN:

20078

American (AMR)

AF:

0.00205

AC:

AN:

6328

Ashkenazi Jewish (ASJ)

AF:

0.00

AC:

AN:

1688

East Asian (EAS)

AF:

0.00

AC:

AN:

3034

South Asian (SAS)

AF:

0.000595

AC:

AN:

1682

European-Finnish (FIN)

AF:

0.00

AC:

AN:

4480

Middle Eastern (MID)

AF:

0.00568

AC:

AN:

176

European-Non Finnish (NFE)

AF:

0.000189

AC:

AN:

36970

Other (OTH)

AF:

0.00207

AC:

AN:

964

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.672

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

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:

0.000595

Hom.:

Bravo

AF:

0.000230

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

BayesDel_noAF

Benign

-0.97

CADD

Benign

2.5

(source)

DANN

Benign

0.52

PhyloP100

0.39

Mutation Taster

=100/0

polymorphism

(source)

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

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

Publications

You must be logged in to view publications. This limit was set because tens of millions (!) of queries from AI bots are generated daily.

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