dbSNP rs3798324: TCP10L3:n.1250T>A (chr6-167373086-A-T) – ACMG Classification: Benign (-8 pts)

Variant summary

Our verdict is Benign. The variant received -8 ACMG points: 0P and 8B. BP4_StrongBS2

The ENST00000397829.9(TCP10L3):n.1250T>A 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 0.0608 in 1,538,184 control chromosomes in the GnomAD database, including 20 homozygotes. 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 0.055 ( 0 hom., cov: 41)

Exomes 𝑓: 0.061 ( 20 hom. )

Consequence

TCP10L3
ENST00000397829.9 non_coding_transcript_exon

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.208

Publications

1 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: Benign. The variant received -8 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.95).

BS2

High Homozygotes in GnomAdExome4 at 20 gene

Transcripts

RefSeq

Gene	Transcript	HGVSc	Effect
TCP10L3	NR_163193.1 link	n.*4T>A	downstream_gene_variant
TCP10L3	NR_163194.1 link	n.*4T>A	downstream_gene_variant
TCP10L3	NR_163195.1 link	n.*4T>A	downstream_gene_variant
TCP10L3	NR_163196.1 link	n.*4T>A	downstream_gene_variant

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TCP10L3	ENST00000397829.9 link	n.1250T>A	non_coding_transcript_exon_variant	Exon 8 of 8	1
TCP10L3	ENST00000463894.7 link	n.3511T>A	non_coding_transcript_exon_variant	Exon 6 of 6	2
TCP10L3	ENST00000617120.5 link	n.889T>A	non_coding_transcript_exon_variant	Exon 6 of 6	5

Frequencies

GnomAD3 genomes

AF:

0.0552

AC:

8345

AN:

151258

Hom.:

Cov.:

show subpopulations

Gnomad AFR

AF:

0.0222

Gnomad AMI

AF:

0.0422

Gnomad AMR

AF:

0.0833

Gnomad ASJ

AF:

0.0838

Gnomad EAS

AF:

0.215

Gnomad SAS

AF:

0.104

Gnomad FIN

AF:

0.0550

Gnomad MID

AF:

0.0255

Gnomad NFE

AF:

0.0525

Gnomad OTH

AF:

0.0550

GnomAD4 exome

AF:

0.0614

AC:

85142

AN:

1386812

Hom.:

Cov.:

AF XY:

0.0623

AC XY:

42593

AN XY:

684150

show subpopulations

⚠️ The allele balance in gnomAD version 4 Exomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0196

AC:

599

AN:

30504

American (AMR)

AF:

0.106

AC:

3255

AN:

30852

Ashkenazi Jewish (ASJ)

AF:

0.0938

AC:

2005

AN:

21386

East Asian (EAS)

AF:

0.195

AC:

7548

AN:

38694

South Asian (SAS)

AF:

0.107

AC:

7808

AN:

73060

European-Finnish (FIN)

AF:

0.0614

AC:

3096

AN:

50410

Middle Eastern (MID)

AF:

0.0487

AC:

258

AN:

5298

European-Non Finnish (NFE)

AF:

0.0524

AC:

56576

AN:

1079640

Other (OTH)

AF:

0.0702

AC:

3997

AN:

56968

⚠️ The allele balance in gnomAD4 Exomes is highly skewed from 0.5 (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.351

Heterozygous variant carriers

4606

9212

13817

18423

23029

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2412

4824

7236

9648

12060

<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

AF:

0.0552

AC:

8362

AN:

151372

Hom.:

Cov.:

AF XY:

0.0582

AC XY:

4304

AN XY:

73988

show subpopulations

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5.

African (AFR)

AF:

0.0224

AC:

928

AN:

41484

American (AMR)

AF:

0.0837

AC:

1266

AN:

15126

Ashkenazi Jewish (ASJ)

AF:

0.0838

AC:

289

AN:

3448

East Asian (EAS)

AF:

0.216

AC:

1094

AN:

5076

South Asian (SAS)

AF:

0.103

AC:

493

AN:

4766

European-Finnish (FIN)

AF:

0.0550

AC:

580

AN:

10542

Middle Eastern (MID)

AF:

0.0240

AC:

AN:

292

European-Non Finnish (NFE)

AF:

0.0525

AC:

3551

AN:

67644

Other (OTH)

AF:

0.0554

AC:

116

AN:

2094

⚠️ The allele balance in gnomAD version 4 Genomes is significantly skewed from the expected value of 0.5. (p-value = 0), which strongly suggests a high chance of mosaicism in these individuals.

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.344

Heterozygous variant carriers

475

950

1426

1901

2376

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Variant carriers

108

216

324

432

540

<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:

0.0523

Hom.:

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.95

CADD

Benign

2.7

(source)

DANN

Benign

0.39

PhyloP100

0.21

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

Publications

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Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

Publications

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over