dbSNP rs9295089: TAGAP:c.148+657A>G (chr6-159042932-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 NM_054114.5(TAGAP):c.148+657A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.189 in 152,602 control chromosomes in the GnomAD database, including 4,422 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 0.19 ( 4419 hom., cov: 33)

Exomes 𝑓: 0.061 ( 3 hom. )

Consequence

TAGAP
NM_054114.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.509

Publications

21 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:

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=-0.91).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.426 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAGAP	NM_054114.5 link	c.148+657A>G		intron_variant	Intron 4 of 9	ENST00000367066.8	NP_473455.2	Q8N103-1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAGAP	ENST00000367066.8 link	c.148+657A>G		intron_variant	Intron 4 of 9	1	NM_054114.5	ENSP00000356033.4		Q8N103-1

Frequencies

GnomAD3 genomes

AF:

0.189

AC:

28758

AN:

152126

Hom.:

4400

Cov.:

show subpopulations

Gnomad AFR

AF:

0.431

Gnomad AMI

AF:

0.193

Gnomad AMR

AF:

0.0947

Gnomad ASJ

AF:

0.0936

Gnomad EAS

AF:

0.0327

Gnomad SAS

AF:

0.0513

Gnomad FIN

AF:

0.0823

Gnomad MID

AF:

0.142

Gnomad NFE

AF:

0.108

Gnomad OTH

AF:

0.152

GnomAD4 exome

AF:

0.0611

AC:

AN:

360

Hom.:

Cov.:

AF XY:

0.0539

AC XY:

AN XY:

204

show subpopulations

African (AFR)

AC:

AN:

American (AMR)

AF:

0.00

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.0526

AC:

AN:

European-Finnish (FIN)

AF:

0.00

AC:

AN:

Middle Eastern (MID)

AC:

AN:

European-Non Finnish (NFE)

AF:

0.0763

AC:

AN:

236

Other (OTH)

AF:

0.00

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.531

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.189

AC:

28824

AN:

152242

Hom.:

4419

Cov.:

AF XY:

0.183

AC XY:

13605

AN XY:

74454

show subpopulations

African (AFR)

AF:

0.432

AC:

17902

AN:

41476

American (AMR)

AF:

0.0946

AC:

1447

AN:

15304

Ashkenazi Jewish (ASJ)

AF:

0.0936

AC:

325

AN:

3472

East Asian (EAS)

AF:

0.0326

AC:

169

AN:

5192

South Asian (SAS)

AF:

0.0513

AC:

248

AN:

4830

European-Finnish (FIN)

AF:

0.0823

AC:

874

AN:

10616

Middle Eastern (MID)

AF:

0.139

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.108

AC:

7323

AN:

68032

Other (OTH)

AF:

0.151

AC:

319

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.501

Heterozygous variant carriers

1038

2076

3115

4153

5191

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

280

560

840

1120

1400

<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:

0.129

Hom.:

3194

Bravo

AF:

0.202

Asia WGS

AF:

0.0580

AC:

204

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.91

CADD

Benign

5.0

(source)

DANN

Benign

0.50

PhyloP100

-0.51

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