Genetic Variant ENST00000645980.2:c.-272+1452A>C (chr6-159094277-T-G) – 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.-272+1452A>C 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 152,342 control chromosomes in the GnomAD database, including 44,638 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 ( 44592 hom., cov: 33)

Exomes 𝑓: 0.76 ( 46 hom. )

Consequence

TAGAP
ENST00000645980.2 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0310

Publications

14 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:

LOC112267968 (HGNC:):

LOC112267968 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=-0.84).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.91 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	HGVSc	Effect	Exon Rank	Protein	UniProt
TAGAP	ENST00000645980.2	c.-272+1452A>C	intron	N/A	ENSP00000520449.1	A0AAQ5BID7
ENSG00000224478	ENST00000642586.1	n.185T>G	non_coding_transcript_exon	Exon 1 of 5
ENSG00000285492	ENST00000642829.1	n.500+1452A>C	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.760

AC:

115566

AN:

152076

Hom.:

44530

Cov.:

show subpopulations

Gnomad AFR

AF:

0.846

Gnomad AMI

AF:

0.575

Gnomad AMR

AF:

0.805

Gnomad ASJ

AF:

0.671

Gnomad EAS

AF:

0.932

Gnomad SAS

AF:

0.792

Gnomad FIN

AF:

0.788

Gnomad MID

AF:

0.671

Gnomad NFE

AF:

0.685

Gnomad OTH

AF:

0.751

GnomAD4 exome

AF:

0.757

AC:

112

AN:

148

Hom.:

Cov.:

AF XY:

0.755

AC XY:

AN XY:

110

show subpopulations

African (AFR)

AF:

1.00

AC:

AN:

American (AMR)

AC:

AN:

Ashkenazi Jewish (ASJ)

AC:

AN:

East Asian (EAS)

AC:

AN:

South Asian (SAS)

AF:

0.900

AC:

AN:

European-Finnish (FIN)

AF:

0.800

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.733

AC:

AN:

116

Other (OTH)

AF:

0.875

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.532

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:

0.760

AC:

115687

AN:

152194

Hom.:

44592

Cov.:

AF XY:

0.768

AC XY:

57171

AN XY:

74412

show subpopulations

African (AFR)

AF:

0.846

AC:

35109

AN:

41494

American (AMR)

AF:

0.805

AC:

12315

AN:

15302

Ashkenazi Jewish (ASJ)

AF:

0.671

AC:

2330

AN:

3472

East Asian (EAS)

AF:

0.932

AC:

4828

AN:

5180

South Asian (SAS)

AF:

0.791

AC:

3815

AN:

4826

European-Finnish (FIN)

AF:

0.788

AC:

8362

AN:

10606

Middle Eastern (MID)

AF:

0.684

AC:

201

AN:

294

European-Non Finnish (NFE)

AF:

0.685

AC:

46609

AN:

67994

Other (OTH)

AF:

0.754

AC:

1594

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.504

Heterozygous variant carriers

1384

2768

4153

5537

6921

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:

0.716

Hom.:

17178

Bravo

AF:

0.764

Asia WGS

AF:

0.883

AC:

3070

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.84

CADD

Benign

4.2

(source)

DANN

Benign

0.52

PhyloP100

-0.031

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