Genetic Variant XM_047419645.1:c.495-37A>G (chr6-159063744-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 XM_047419645.1(LOC112267968):c.495-37A>G 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 152,598 control chromosomes in the GnomAD database, including 44,530 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 ( 44389 hom., cov: 31)

Exomes 𝑓: 0.74 ( 141 hom. )

Consequence

LOC112267968
XM_047419645.1 intron

Scores

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -1.79

Publications

13 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:

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=-0.93).

BA1

GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.897 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+1024A>G	intron	N/A	ENSP00000520449.1	A0AAQ5BID7
TAGAP-AS1	ENST00000606470.2	TSL:5	n.541-1135T>C	intron	N/A
ENSG00000285492	ENST00000642829.1		n.672-37A>G	intron	N/A

Frequencies

GnomAD3 genomes

AF:

0.760

AC:

115585

AN:

151986

Hom.:

44346

Cov.:

show subpopulations

Gnomad AFR

AF:

0.803

Gnomad AMI

AF:

0.701

Gnomad AMR

AF:

0.792

Gnomad ASJ

AF:

0.732

Gnomad EAS

AF:

0.919

Gnomad SAS

AF:

0.817

Gnomad FIN

AF:

0.809

Gnomad MID

AF:

0.706

Gnomad NFE

AF:

0.707

Gnomad OTH

AF:

0.754

GnomAD4 exome

AF:

0.744

AC:

366

AN:

492

Hom.:

141

Cov.:

AF XY:

0.750

AC XY:

246

AN XY:

328

show subpopulations

African (AFR)

AF:

0.875

AC:

AN:

American (AMR)

AF:

0.875

AC:

AN:

Ashkenazi Jewish (ASJ)

AF:

0.625

AC:

AN:

East Asian (EAS)

AF:

0.800

AC:

AN:

South Asian (SAS)

AF:

1.00

AC:

AN:

European-Finnish (FIN)

AF:

0.756

AC:

AN:

Middle Eastern (MID)

AF:

0.500

AC:

AN:

European-Non Finnish (NFE)

AF:

0.723

AC:

243

AN:

336

Other (OTH)

AF:

0.833

AC:

AN:

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.492

Heterozygous variant carriers

0.00

0.20

0.40

0.60

0.80

0.95

Allele balance

Age Distribution

Exome Het

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:

0.761

AC:

115679

AN:

152106

Hom.:

44389

Cov.:

AF XY:

0.769

AC XY:

57175

AN XY:

74368

show subpopulations

African (AFR)

AF:

0.803

AC:

33298

AN:

41478

American (AMR)

AF:

0.792

AC:

12109

AN:

15284

Ashkenazi Jewish (ASJ)

AF:

0.732

AC:

2541

AN:

3472

East Asian (EAS)

AF:

0.919

AC:

4756

AN:

5174

South Asian (SAS)

AF:

0.816

AC:

3928

AN:

4816

European-Finnish (FIN)

AF:

0.809

AC:

8570

AN:

10598

Middle Eastern (MID)

AF:

0.707

AC:

208

AN:

294

European-Non Finnish (NFE)

AF:

0.707

AC:

48030

AN:

67966

Other (OTH)

AF:

0.757

AC:

1601

AN:

2114

Allele Balance Distribution

Red line indicates average allele balance

Average allele balance: 0.505

Heterozygous variant carriers

1398

2796

4195

5593

6991

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:

0.724

Hom.:

168872

Bravo

AF:

0.762

Asia WGS

AF:

0.879

AC:

3058

AN:

3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.45

(source)

DANN

Benign

0.39

PhyloP100

-1.8

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