Genetic Variant TAGAP:c.149-176G>A (chr6-159042420-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 NM_054114.5(TAGAP):c.149-176G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0857 in 1,383,692 control chromosomes in the GnomAD database, including 9,578 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 0.16 ( 3993 hom., cov: 32)

Exomes 𝑓: 0.076 ( 5585 hom. )

Consequence

TAGAP
NM_054114.5 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.00500

Publications

20 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:

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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=-0.65).

BA1

GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.42 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_054114.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TAGAP	NM_054114.5	MANE Select	c.149-176G>A	intron	N/A	NP_473455.2
TAGAP	NM_152133.3		c.-219-905G>A	intron	N/A	NP_687034.1	Q8N103-2
TAGAP	NM_138810.4		c.149-176G>A	intron	N/A	NP_620165.1	Q8N103-4

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TAGAP	ENST00000367066.8	TSL:1 MANE Select	c.149-176G>A	intron	N/A	ENSP00000356033.4	Q8N103-1
TAGAP	ENST00000338313.5	TSL:1	c.149-176G>A	intron	N/A	ENSP00000340217.5	Q8N103-4
TAGAP	ENST00000865619.1		c.149-176G>A	intron	N/A	ENSP00000535678.1

Frequencies

GnomAD3 genomes

AF:

0.162

AC:

24686

AN:

151998

Hom.:

3975

Cov.:

show subpopulations

Gnomad AFR

AF:

0.424

Gnomad AMI

AF:

0.0965

Gnomad AMR

AF:

0.0627

Gnomad ASJ

AF:

0.0553

Gnomad EAS

AF:

0.0321

Gnomad SAS

AF:

0.0408

Gnomad FIN

AF:

0.0626

Gnomad MID

AF:

0.0949

Gnomad NFE

AF:

0.0678

Gnomad OTH

AF:

0.122

GnomAD4 exome

AF:

0.0762

AC:

93871

AN:

1231576

Hom.:

5585

Cov.:

AF XY:

0.0750

AC XY:

44771

AN XY:

596886

show subpopulations

African (AFR)

AF:

0.429

AC:

11777

AN:

27482

American (AMR)

AF:

0.0532

AC:

887

AN:

16680

Ashkenazi Jewish (ASJ)

AF:

0.0601

AC:

1088

AN:

18106

East Asian (EAS)

AF:

0.0251

AC:

846

AN:

33732

South Asian (SAS)

AF:

0.0497

AC:

2759

AN:

55472

European-Finnish (FIN)

AF:

0.0584

AC:

1671

AN:

28628

Middle Eastern (MID)

AF:

0.0688

AC:

237

AN:

3444

European-Non Finnish (NFE)

AF:

0.0708

AC:

70551

AN:

997072

Other (OTH)

AF:

0.0796

AC:

4055

AN:

50960

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.498

Heterozygous variant carriers

3866

7732

11597

15463

19329

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

Exome Hom

Variant carriers

2996

5992

8988

11984

14980

<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:

0.163

AC:

24753

AN:

152116

Hom.:

3993

Cov.:

AF XY:

0.158

AC XY:

11725

AN XY:

74358

show subpopulations

African (AFR)

AF:

0.425

AC:

17598

AN:

41420

American (AMR)

AF:

0.0626

AC:

958

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.0553

AC:

192

AN:

3470

East Asian (EAS)

AF:

0.0320

AC:

166

AN:

5186

South Asian (SAS)

AF:

0.0408

AC:

197

AN:

4824

European-Finnish (FIN)

AF:

0.0626

AC:

664

AN:

10600

Middle Eastern (MID)

AF:

0.0918

AC:

AN:

294

European-Non Finnish (NFE)

AF:

0.0678

AC:

4608

AN:

67996

Other (OTH)

AF:

0.121

AC:

255

AN:

2112

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.502

Heterozygous variant carriers

853

1706

2560

3413

4266

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

236

472

708

944

1180

<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:

0.0899

Hom.:

5328

Bravo

AF:

0.175

Asia WGS

AF:

0.0520

AC:

182

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.65

CADD

Benign

(source)

DANN

Benign

0.87

PhyloP100

-0.0050

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over