Genetic Variant TAGAP:c.-101+1024A>G (chr6-159063744-T-C) – ACMG Classification: Benign (-12 pts)

Variant summary

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

The ENST00000645980.2(TAGAP):c.-101+1024A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.76 in 152,598 control chromosomes in the GnomAD database, including 44,530 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 0.76 ( 44389 hom., cov: 31)

Exomes 𝑓: 0.74 ( 141 hom. )

Consequence

TAGAP
ENST00000645980.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

Publications

13 publications found

Variant links:

Genes affected

TAGAP (HGNC:15669): (T cell activation RhoGTPase activating protein) This gene encodes a member of the Rho GTPase-activator protein superfamily. The encoded protein may function as a Rho GTPase-activating protein. Alterations in this gene may be associated with several diseases, including rheumatoid arthritis, celiac disease, and multiple sclerosis. Alternate splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2013]

TAGAP links:

TAGAP-AS1 (HGNC:55239): (TAGAP antisense RNA 1)

TAGAP-AS1 links:

ENSG00000285492 (HGNC:):

ENSG00000285492 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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
LOC112267968	XM_047419645.1 link	c.495-37A>G		intron_variant	Intron 4 of 4		XP_047275601.1

Ensembl

Gene	Transcript	HGVSc	Effect	Exon rank	TSL	Protein
TAGAP	ENST00000645980.2 link	c.-101+1024A>G	intron_variant	Intron 2 of 6		ENSP00000520449.1
TAGAP-AS1	ENST00000606470.2 link	n.541-1135T>C	intron_variant	Intron 2 of 2	5
ENSG00000285492	ENST00000642829.1 link	n.672-37A>G	intron_variant	Intron 4 of 4

Frequencies

GnomAD3 genomes

AF:

0.760

AC:

115585

AN:

151986

Hom.:

44346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.803

Gnomad AMI

AF:

0.701

Gnomad AMR

AF:

0.792

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.919

Gnomad SAS

AF:

0.817

Gnomad FIN

AF:

0.809

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.707

Gnomad OTH

AF:

0.754

GnomAD4 exome

AF:

0.744

AC:

366

AN:

492

Hom.:

141

Cov.:

AF XY:

0.750

AC XY:

246

AN XY:

328

show subpopulations

African (AFR)

AF:

0.875

AC:

AN:

American (AMR)

AF:

0.875

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.625

AC:

AN:

East Asian (EAS)

AF:

0.800

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.756

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.723

AC:

243

AN:

336

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

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

AF:

0.761

AC:

115679

AN:

152106

Hom.:

44389

Cov.:

AF XY:

0.769

AC XY:

57175

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.803

AC:

33298

AN:

41478

American (AMR)

AF:

0.792

AC:

12109

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.732

AC:

2541

AN:

3472

East Asian (EAS)

AF:

0.919

AC:

4756

AN:

5174

South Asian (SAS)

AF:

0.816

AC:

3928

AN:

4816

European-Finnish (FIN)

AF:

0.809

AC:

8570

AN:

10598

Middle Eastern (MID)

AF:

0.707

AC:

208

AN:

294

European-Non Finnish (NFE)

AF:

0.707

AC:

48030

AN:

67966

Other (OTH)

AF:

0.757

AC:

1601

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1398

2796

4195

5593

6991

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

856

1712

2568

3424

4280

<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:

0.724

Hom.:

168872

Bravo

AF:

0.762

Asia WGS

AF:

0.879

AC:

3058

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.45

(source)

DANN

Benign

0.39

PhyloP100

-1.8

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