rs1340668

Variant names:

• chr6-54318518-C-T
• rs1340668
• NM_014464.4:c.356-2061C>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.356-2061C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0358 in 152,190 control chromosomes in the GnomAD database, including 166 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 0.036 (166 hom., cov: 32)
• Consequence: TINAG NM_014464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.28
• Publications: 1 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=-0.97).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.0989 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
TINAG	NM_014464.4	c.356-2061C>T		intron_variant	Intron 1 of 10	ENST00000259782.9	NP_055279.3

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
TINAG	ENST00000259782.9	c.356-2061C>T		intron_variant	Intron 1 of 10	1	NM_014464.4	ENSP00000259782.4
TINAG	ENST00000370869.7	c.344-2061C>T		intron_variant	Intron 2 of 5	3		ENSP00000359906.3
TINAG	ENST00000370864.3	c.302-2061C>T		intron_variant	Intron 1 of 3	2		ENSP00000359901.3
TINAG	ENST00000486436.1	n.418-2061C>T		intron_variant	Intron 2 of 4	3

Frequencies

GnomAD3 genomes AF: 0.0358 AC: 5441 AN: 152072 Hom.: 162 Cov.: 32

Gnomad AFR AF: 0.0512

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.0814

Gnomad ASJ AF: 0.0346

Gnomad EAS AF: 0.107

Gnomad SAS AF: 0.0149

Gnomad FIN AF: 0.00499

Gnomad MID AF: 0.0506

Gnomad NFE AF: 0.0173

Gnomad OTH AF: 0.0426

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

GnomAD4 genome AF: 0.0358 AC: 5450 AN: 152190 Hom.: 166 Cov.: 32 AF XY: 0.0362 AC XY: 2696 AN XY: 74396

African (AFR) AF: 0.0513 AC: 2129 AN: 41526

American (AMR) AF: 0.0811 AC: 1238 AN: 15262

Ashkenazi Jewish (ASJ) AF: 0.0346 AC: 120 AN: 3468

East Asian (EAS) AF: 0.106 AC: 549 AN: 5168

South Asian (SAS) AF: 0.0154 AC: 74 AN: 4816

European-Finnish (FIN) AF: 0.00499 AC: 53 AN: 10612

Middle Eastern (MID) AF: 0.0510 AC: 15 AN: 294

European-Non Finnish (NFE) AF: 0.0173 AC: 1179 AN: 68022

Other (OTH) AF: 0.0441 AC: 93 AN: 2110

Alfa AF: 0.0333 Hom.: 94

Bravo AF: 0.0453

Asia WGS AF: 0.0680 AC: 235 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.21
DANN	Benign	0.44
PhyloP100		-1.3
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: rs1340668; hg19: chr6-54183316;