Genetic Variant TCL6:n.317-123C>T (chr14-95641618-C-T) – ACMG Classification: Benign (-12 pts)

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000555032.2(TCL6):n.317-123C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.117 in 152,176 control chromosomes in the GnomAD database, including 1,207 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 0.12 ( 1206 hom., cov: 32)

Exomes 𝑓: 0.11 ( 1 hom. )

Consequence

TCL6
ENST00000555032.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0590

Publications

9 publications found

Variant links:

Genes affected

TCL6 (HGNC:13463): (T cell leukemia/lymphoma 6)

TCL6 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -12 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.89).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.179 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL
TCL6	ENST00000555032.2 link	n.317-123C>T	intron_variant	Intron 2 of 3	4
TCL6	ENST00000655483.1 link	n.103-123C>T	intron_variant	Intron 1 of 2
TCL6	ENST00000661620.1 link	n.188-123C>T	intron_variant	Intron 1 of 2

Frequencies

GnomAD3 genomes

AF:

0.117

AC:

17805

AN:

152040

Hom.:

1202

Cov.:

show subpopulations

Gnomad AFR

AF:

0.183

Gnomad AMI

AF:

0.0252

Gnomad AMR

AF:

0.0926

Gnomad ASJ

AF:

0.0988

Gnomad EAS

AF:

0.106

Gnomad SAS

AF:

0.175

Gnomad FIN

AF:

0.0858

Gnomad MID

AF:

0.187

Gnomad NFE

AF:

0.0859

Gnomad OTH

AF:

0.129

GnomAD4 exome

AF:

0.111

AC:

AN:

Hom.:

AF XY:

0.00

AC XY:

AN XY:

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.00

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.200

AC:

AN:

Other (OTH)

AF:

0.00

AC:

AN:

Age Distribution

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

AF:

0.117

AC:

17828

AN:

152158

Hom.:

1206

Cov.:

AF XY:

0.117

AC XY:

8685

AN XY:

74396

show subpopulations

African (AFR)

AF:

0.183

AC:

7575

AN:

41472

American (AMR)

AF:

0.0926

AC:

1415

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.0988

AC:

343

AN:

3472

East Asian (EAS)

AF:

0.106

AC:

550

AN:

5178

South Asian (SAS)

AF:

0.175

AC:

842

AN:

4824

European-Finnish (FIN)

AF:

0.0858

AC:

910

AN:

10606

Middle Eastern (MID)

AF:

0.194

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0859

AC:

5842

AN:

68006

Other (OTH)

AF:

0.128

AC:

271

AN:

2110

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

785

1570

2355

3140

3925

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

210

420

630

840

1050

<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:

0.0904

Hom.:

1189

Bravo

AF:

0.119

Asia WGS

AF:

0.126

AC:

437

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.6

(source)

DANN

Benign

0.77

PhyloP100

-0.059

Mutation Taster

=100/0

polymorphism

(source)

Splicing

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