rs17828521

Positions:

• chr6-54355445-C-T

Variant summary

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

The NM_014464.4(TINAG):​c.1250+809C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0574 in 151,874 control chromosomes in the GnomAD database, including 467 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 0.057 (467 hom., cov: 32)
• Consequence: TINAG NM_014464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.249

Genes affected

TINAG (HGNC:14599): (tubulointerstitial nephritis antigen) This gene encodes a glycoprotein that is restricted within the kidney to the basement membranes underlying the epithelium of Bowman's capsule and proximal and distal tubules. Autoantibodies against this protein are found in sera of patients with tubulointerstital nephritis, membranous nephropathy and anti-glomerular basement membrane nephritis. Ontogeny studies suggest that the expression of this antigen is developmentally regulated in a precise spatial and temporal pattern throughout nephrogenesis. [provided by RefSeq, Nov 2011]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TINAG	NM_014464.4	c.1250+809C>T		intron_variant		ENST00000259782.9	NP_055279.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TINAG	ENST00000259782.9	c.1250+809C>T		intron_variant		1	NM_014464.4	ENSP00000259782.4

Frequencies

GnomAD3 genomes AF: 0.0575 AC: 8726 AN: 151756 Hom.: 465 Cov.: 32

Gnomad AFR AF: 0.0784

Gnomad AMI AF: 0.0429

Gnomad AMR AF: 0.0338

Gnomad ASJ AF: 0.0459

Gnomad EAS AF: 0.293

Gnomad SAS AF: 0.0471

Gnomad FIN AF: 0.0401

Gnomad MID AF: 0.0728

Gnomad NFE AF: 0.0363

Gnomad OTH AF: 0.0618

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.0574 AC: 8724 AN: 151874 Hom.: 467 Cov.: 32 AF XY: 0.0585 AC XY: 4340 AN XY: 74206

Gnomad4 AFR AF: 0.0782

Gnomad4 AMR AF: 0.0336

Gnomad4 ASJ AF: 0.0459

Gnomad4 EAS AF: 0.294

Gnomad4 SAS AF: 0.0465

Gnomad4 FIN AF: 0.0401

Gnomad4 NFE AF: 0.0363

Gnomad4 OTH AF: 0.0616

Alfa AF: 0.0402 Hom.: 409

Bravo AF: 0.0583

Asia WGS AF: 0.167 AC: 581 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.69

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: rs17828521; hg19: chr6-54220243;