dbSNP rs6752614: TIGD1:p.Ala274Ala (chr2-232549061-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.822G>A(p.Ala274Ala) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.49 in 712,134 control chromosomes in the GnomAD database, including 88,489 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 0.44 ( 15564 hom., cov: 33)

Exomes 𝑓: 0.50 ( 72925 hom. )

Consequence

TIGD1
NM_145702.4 synonymous

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.28

Publications

5 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=-0.58).

BP7

Synonymous conserved (PhyloP=-1.28 with no splicing effect.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.564 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TIGD1	NM_145702.4 link	c.822G>A	p.Ala274Ala	synonymous_variant	Exon 1 of 1	ENST00000408957.7	NP_663748.1	Q96MW7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TIGD1	ENST00000408957.7 link	c.822G>A	p.Ala274Ala	synonymous_variant	Exon 1 of 1	6	NM_145702.4	ENSP00000386186.3		Q96MW7

Frequencies

GnomAD3 genomes

AF:

0.438

AC:

66521

AN:

151982

Hom.:

15552

Cov.:

show subpopulations

Gnomad AFR

AF:

0.272

Gnomad AMI

AF:

0.474

Gnomad AMR

AF:

0.573

Gnomad ASJ

AF:

0.545

Gnomad EAS

AF:

0.574

Gnomad SAS

AF:

0.580

Gnomad FIN

AF:

0.465

Gnomad MID

AF:

0.541

Gnomad NFE

AF:

0.475

Gnomad OTH

AF:

0.478

GnomAD2 exomes

AF:

0.523

AC:

77634

AN:

148544

AF XY:

0.525

show subpopulations

Gnomad AFR exome

AF:

0.260

Gnomad AMR exome

AF:

0.663

Gnomad ASJ exome

AF:

0.557

Gnomad EAS exome

AF:

0.576

Gnomad FIN exome

AF:

0.469

Gnomad NFE exome

AF:

0.478

Gnomad OTH exome

AF:

0.526

GnomAD4 exome

AF:

0.504

AC:

282133

AN:

560034

Hom.:

72925

Cov.:

AF XY:

0.509

AC XY:

153605

AN XY:

301972

show subpopulations

African (AFR)

AF:

0.268

AC:

4199

AN:

15650

American (AMR)

AF:

0.653

AC:

22329

AN:

34220

Ashkenazi Jewish (ASJ)

AF:

0.555

AC:

10898

AN:

19646

East Asian (EAS)

AF:

0.581

AC:

18597

AN:

32024

South Asian (SAS)

AF:

0.579

AC:

35600

AN:

61522

European-Finnish (FIN)

AF:

0.468

AC:

22711

AN:

48546

Middle Eastern (MID)

AF:

0.536

AC:

1294

AN:

2416

European-Non Finnish (NFE)

AF:

0.480

AC:

151519

AN:

315692

Other (OTH)

AF:

0.494

AC:

14986

AN:

30318

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.472

Heterozygous variant carriers

6167

12335

18502

24670

30837

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

792

1584

2376

3168

3960

<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:

0.438

AC:

66552

AN:

152100

Hom.:

15564

Cov.:

AF XY:

0.442

AC XY:

32889

AN XY:

74362

show subpopulations

African (AFR)

AF:

0.272

AC:

11284

AN:

41478

American (AMR)

AF:

0.574

AC:

8773

AN:

15280

Ashkenazi Jewish (ASJ)

AF:

0.545

AC:

1892

AN:

3470

East Asian (EAS)

AF:

0.573

AC:

2961

AN:

5170

South Asian (SAS)

AF:

0.580

AC:

2796

AN:

4824

European-Finnish (FIN)

AF:

0.465

AC:

4907

AN:

10562

Middle Eastern (MID)

AF:

0.541

AC:

159

AN:

294

European-Non Finnish (NFE)

AF:

0.475

AC:

32328

AN:

67998

Other (OTH)

AF:

0.483

AC:

1021

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.503

Heterozygous variant carriers

1872

3744

5617

7489

9361

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

624

1248

1872

2496

3120

<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:

0.477

Hom.:

5691

Bravo

AF:

0.441

Asia WGS

AF:

0.594

AC:

2067

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.58

CADD

Benign

3.3

(source)

DANN

Benign

0.91

PhyloP100

-1.3

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

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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