Genetic Variant TIGD1:p.Lys84Lys (chr2-232549631-C-T) – ACMG Classification: Benign (-13 pts)

Variant summary

Our verdict is Benign. The variant received -13 ACMG points: 0P and 13B. BP4_StrongBP7BA1

The NM_145702.4(TIGD1):c.252G>A(p.Lys84Lys) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.457 in 706,670 control chromosomes in the GnomAD database, including 76,909 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 0.40 ( 13214 hom., cov: 33)

Exomes 𝑓: 0.47 ( 63695 hom. )

Consequence

TIGD1
NM_145702.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.372

Publications

6 publications found

Variant links:

Genes affected

TIGD1 (HGNC:14523): (tigger transposable element derived 1) The protein encoded by this gene belongs to the tigger subfamily of the pogo superfamily of DNA-mediated transposons in humans. These proteins are related to DNA transposons found in fungi and nematodes, and more distantly to the Tc1 and mariner transposases. They are also very similar to the major mammalian centromere protein B. The exact function of this gene is not known. [provided by RefSeq, Jul 2008]

TIGD1 links:

Genome browser will be placed here

ACMG classification

Classification was made for transcript

Our verdict: Benign. The variant received -13 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.49).

BP7

Synonymous conserved (PhyloP=-0.372 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.533 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TIGD1	NM_145702.4 link	c.252G>A	p.Lys84Lys	synonymous_variant	Exon 1 of 1	ENST00000408957.7	NP_663748.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TIGD1	ENST00000408957.7 link	c.252G>A	p.Lys84Lys	synonymous_variant	Exon 1 of 1	6	NM_145702.4	ENSP00000386186.3

Frequencies

GnomAD3 genomes

AF:

0.396

AC:

60214

AN:

151954

Hom.:

13199

Cov.:

show subpopulations

Gnomad AFR

AF:

0.198

Gnomad AMI

AF:

0.472

Gnomad AMR

AF:

0.522

Gnomad ASJ

AF:

0.540

Gnomad EAS

AF:

0.472

Gnomad SAS

AF:

0.551

Gnomad FIN

AF:

0.430

Gnomad MID

AF:

0.529

Gnomad NFE

AF:

0.457

Gnomad OTH

AF:

0.431

GnomAD2 exomes

AF:

0.490

AC:

67051

AN:

136798

AF XY:

0.494

show subpopulations

Gnomad AFR exome

AF:

0.187

Gnomad AMR exome

AF:

0.596

Gnomad ASJ exome

AF:

0.550

Gnomad EAS exome

AF:

0.501

Gnomad FIN exome

AF:

0.442

Gnomad NFE exome

AF:

0.458

Gnomad OTH exome

AF:

0.494

GnomAD4 exome

AF:

0.473

AC:

262380

AN:

554598

Hom.:

63695

Cov.:

AF XY:

0.479

AC XY:

143519

AN XY:

299628

show subpopulations

African (AFR)

AF:

0.195

AC:

3070

AN:

15758

American (AMR)

AF:

0.587

AC:

20201

AN:

34434

Ashkenazi Jewish (ASJ)

AF:

0.547

AC:

10755

AN:

19666

East Asian (EAS)

AF:

0.472

AC:

15162

AN:

32110

South Asian (SAS)

AF:

0.549

AC:

33826

AN:

61592

European-Finnish (FIN)

AF:

0.437

AC:

17692

AN:

40528

Middle Eastern (MID)

AF:

0.514

AC:

1254

AN:

2440

European-Non Finnish (NFE)

AF:

0.461

AC:

146416

AN:

317668

Other (OTH)

AF:

0.461

AC:

14004

AN:

30402

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.486

Heterozygous variant carriers

7138

14276

21414

28552

35690

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

762

1524

2286

3048

3810

<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:

0.396

AC:

60234

AN:

152072

Hom.:

13214

Cov.:

AF XY:

0.401

AC XY:

29783

AN XY:

74320

show subpopulations

African (AFR)

AF:

0.197

AC:

8196

AN:

41516

American (AMR)

AF:

0.523

AC:

7991

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.540

AC:

1874

AN:

3470

East Asian (EAS)

AF:

0.472

AC:

2439

AN:

5168

South Asian (SAS)

AF:

0.550

AC:

2653

AN:

4824

European-Finnish (FIN)

AF:

0.430

AC:

4531

AN:

10528

Middle Eastern (MID)

AF:

0.527

AC:

154

AN:

292

European-Non Finnish (NFE)

AF:

0.457

AC:

31046

AN:

67968

Other (OTH)

AF:

0.436

AC:

921

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1768

3536

5304

7072

8840

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

580

1160

1740

2320

2900

<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:

0.383

Hom.:

1954

Bravo

AF:

0.395

Asia WGS

AF:

0.540

AC:

1879

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.49

CADD

Benign

8.6

(source)

DANN

Benign

0.93

PhyloP100

-0.37

Mutation Taster

=100/0

polymorphism (auto)

(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

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over