6-159042420-C-T

Variant names:

• chr6-159042420-C-T
• rs926657
• NM_054114.5:c.149-176G>A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

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
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.00500

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-AS1 (HGNC:55239): (TAGAP antisense RNA 1)

ACMG classification

Verdict is Benign. Variant got -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	c.149-176G>A		intron_variant	Intron 4 of 9	ENST00000367066.8	NP_473455.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TAGAP	ENST00000367066.8	c.149-176G>A		intron_variant	Intron 4 of 9	1	NM_054114.5	ENSP00000356033.4

Frequencies

GnomAD3 genomes AF: 0.162 AC: 24686 AN: 151998 Hom.: 3975 Cov.: 32

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.: 20 AF XY: 0.0750 AC XY: 44771 AN XY: 596886

Gnomad4 AFR exome AF: 0.429

Gnomad4 AMR exome AF: 0.0532

Gnomad4 ASJ exome AF: 0.0601

Gnomad4 EAS exome AF: 0.0251

Gnomad4 SAS exome AF: 0.0497

Gnomad4 FIN exome AF: 0.0584

Gnomad4 NFE exome AF: 0.0708

Gnomad4 OTH exome AF: 0.0796

GnomAD4 genome AF: 0.163 AC: 24753 AN: 152116 Hom.: 3993 Cov.: 32 AF XY: 0.158 AC XY: 11725 AN XY: 74358

Gnomad4 AFR AF: 0.425

Gnomad4 AMR AF: 0.0626

Gnomad4 ASJ AF: 0.0553

Gnomad4 EAS AF: 0.0320

Gnomad4 SAS AF: 0.0408

Gnomad4 FIN AF: 0.0626

Gnomad4 NFE AF: 0.0678

Gnomad4 OTH AF: 0.121

Alfa AF: 0.0688 Hom.: 1143

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	11
DANN	Benign	0.87

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

LitVar

Other links and lift over

dbSNP: rs926657; hg19: chr6-159463452;