Genetic Variant TAGAP:c.-101+3279G>A (chr6-159061489-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 ENST00000645980.2(TAGAP):c.-101+3279G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.69 in 152,006 control chromosomes in the GnomAD database, including 37,084 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 0.69 ( 37009 hom., cov: 30)

Exomes 𝑓: 0.74 ( 75 hom. )

Consequence

TAGAP
ENST00000645980.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.706

Publications

33 publications found

Variant links:

COSMIC-nc: COSV71541262

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:

ENSG00000285492 (HGNC:):

ENSG00000285492 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=-0.89).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.898 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000645980.2. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Gene	Transcript	Tags	HGVSc	Effect	Exon Rank	Protein	UniProt
TAGAP	ENST00000645980.2		c.-101+3279G>A	intron	N/A	ENSP00000520449.1	A0AAQ5BID7
ENSG00000285492	ENST00000642829.1		n.2890G>A	non_coding_transcript_exon	Exon 5 of 5
TAGAP-AS1	ENST00000606470.2	TSL:5	n.541-3390C>T	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.690

AC:

104679

AN:

151632

Hom.:

36981

Cov.:

show subpopulations

Gnomad AFR

AF:

0.554

Gnomad AMI

AF:

0.703

Gnomad AMR

AF:

0.757

Gnomad ASJ

AF:

0.682

Gnomad EAS

AF:

0.920

Gnomad SAS

AF:

0.829

Gnomad FIN

AF:

0.810

Gnomad MID

AF:

0.602

Gnomad NFE

AF:

0.713

Gnomad OTH

AF:

0.686

GnomAD4 exome

AF:

0.742

AC:

190

AN:

256

Hom.:

Cov.:

AF XY:

0.723

AC XY:

149

AN XY:

206

show subpopulations

African (AFR)

AF:

0.375

AC:

AN:

American (AMR)

AF:

0.750

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.667

AC:

AN:

East Asian (EAS)

AF:

1.00

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.833

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.764

AC:

159

AN:

208

Other (OTH)

AF:

0.250

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.448

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

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:

0.690

AC:

104751

AN:

151750

Hom.:

37009

Cov.:

AF XY:

0.700

AC XY:

51935

AN XY:

74142

show subpopulations

African (AFR)

AF:

0.554

AC:

22870

AN:

41294

American (AMR)

AF:

0.758

AC:

11569

AN:

15266

Ashkenazi Jewish (ASJ)

AF:

0.682

AC:

2365

AN:

3468

East Asian (EAS)

AF:

0.920

AC:

4730

AN:

5142

South Asian (SAS)

AF:

0.828

AC:

3983

AN:

4810

European-Finnish (FIN)

AF:

0.810

AC:

8522

AN:

10524

Middle Eastern (MID)

AF:

0.610

AC:

178

AN:

292

European-Non Finnish (NFE)

AF:

0.713

AC:

48445

AN:

67944

Other (OTH)

AF:

0.690

AC:

1451

AN:

2102

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.514

Heterozygous variant carriers

1590

3180

4769

6359

7949

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Genome Het

Genome Hom

Variant carriers

818

1636

2454

3272

4090

<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:

0.703

Hom.:

56607

Bravo

AF:

0.679

Asia WGS

AF:

0.866

AC:

3013

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.89

CADD

Benign

1.1

(source)

DANN

Benign

0.75

PhyloP100

-0.71

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

Variant Effect in Transcripts

RefSeq Transcripts

Ensembl Transcripts

Frequencies

Age Distribution

Age Distribution

ClinVar

Computational scores

Splicing

Publications

Other links and lift over