6-54388283-C-T

Variant names:

• chr6-54388283-C-T
• rs9474831
• NM_014464.4:c.1297-1508C>T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_014464.4(TINAG):​c.1297-1508C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0861 in 152,122 control chromosomes in the GnomAD database, including 1,003 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 0.086 (1003 hom., cov: 32)
• Consequence: TINAG NM_014464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.675
• Publications: 2 publications found

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

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.9).
• 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 rank	MANE	Protein	UniProt
TINAG	NM_014464.4	c.1297-1508C>T		intron_variant	Intron 10 of 10	ENST00000259782.9	NP_055279.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TINAG	ENST00000259782.9	c.1297-1508C>T		intron_variant	Intron 10 of 10	1	NM_014464.4	ENSP00000259782.4

Frequencies

GnomAD3 genomes AF: 0.0861 AC: 13082 AN: 152004 Hom.: 998 Cov.: 32

Gnomad AFR AF: 0.176

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0449

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.294

Gnomad SAS AF: 0.0477

Gnomad FIN AF: 0.0400

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0369

Gnomad OTH AF: 0.0789

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

GnomAD4 genome AF: 0.0861 AC: 13098 AN: 152122 Hom.: 1003 Cov.: 32 AF XY: 0.0860 AC XY: 6398 AN XY: 74368

African (AFR) AF: 0.176 AC: 7320 AN: 41490

American (AMR) AF: 0.0447 AC: 683 AN: 15270

Ashkenazi Jewish (ASJ) AF: 0.0545 AC: 189 AN: 3470

East Asian (EAS) AF: 0.295 AC: 1521 AN: 5160

South Asian (SAS) AF: 0.0469 AC: 226 AN: 4816

European-Finnish (FIN) AF: 0.0400 AC: 424 AN: 10608

Middle Eastern (MID) AF: 0.0748 AC: 22 AN: 294

European-Non Finnish (NFE) AF: 0.0369 AC: 2509 AN: 67990

Other (OTH) AF: 0.0781 AC: 165 AN: 2112

Alfa AF: 0.0461 Hom.: 137

Bravo AF: 0.0910

Asia WGS AF: 0.175 AC: 608 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
CADD	Benign	0.69
DANN	Benign	0.40
PhyloP100		-0.68
Mutation Taster		=100/0	polymorphism (auto)

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

Other links and lift over

dbSNP: rs9474831; hg19: chr6-54253081;