Genetic Variant NM_054114.5: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.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TAGAP	NM_054114.5 link	c.149-176G>A		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.149-176G>A		intron_variant	Intron 4 of 9	1	NM_054114.5	ENSP00000356033.4		Q8N103-1

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 v4.3

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

Transcripts

RefSeq

Ensembl

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over