chr6-54355445-C-T

Variant names:

• chr6-54355445-C-T
• rs17828521
• NM_014464.4:c.1250+809C>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.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
• 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=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.282 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_014464.4. 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
	TINAG	NM_014464.4	MANE Select	c.1250+809C>T		intron	N/A	NP_055279.3

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TINAG	ENST00000259782.9	TSL:1 MANE Select	c.1250+809C>T		intron	N/A	ENSP00000259782.4	Q9UJW2-1

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

African (AFR) AF: 0.0782 AC: 3246 AN: 41486

American (AMR) AF: 0.0336 AC: 511 AN: 15208

Ashkenazi Jewish (ASJ) AF: 0.0459 AC: 159 AN: 3464

East Asian (EAS) AF: 0.294 AC: 1505 AN: 5120

South Asian (SAS) AF: 0.0465 AC: 224 AN: 4814

European-Finnish (FIN) AF: 0.0401 AC: 425 AN: 10590

Middle Eastern (MID) AF: 0.0714 AC: 21 AN: 294

European-Non Finnish (NFE) AF: 0.0363 AC: 2464 AN: 67878

Other (OTH) AF: 0.0616 AC: 130 AN: 2110

Alfa AF: 0.0427 Hom.: 965

Bravo AF: 0.0583

Asia WGS AF: 0.167 AC: 581 AN: 3474

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	5.8
DANN	Benign	0.69
PhyloP100		-0.25
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: rs17828521; hg19: chr6-54220243;