6-54379394-A-G

Variant names:

• chr6-54379394-A-G
• rs9395950
• NM_014464.4:c.1251-1132A>G

Variant summary

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

The NM_014464.4(TINAG):​c.1251-1132A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0952 in 152,200 control chromosomes in the GnomAD database, including 1,159 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 0.095 (1159 hom., cov: 32)
• Consequence: TINAG NM_014464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0550
• 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=-0.92).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.331 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

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TINAG	NM_014464.4	MANE Select	c.1251-1132A>G		intron	N/A	NP_055279.3

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	TINAG	ENST00000259782.9	TSL:1 MANE Select	c.1251-1132A>G		intron	N/A	ENSP00000259782.4

Frequencies

GnomAD3 genomes AF: 0.0951 AC: 14461 AN: 152084 Hom.: 1153 Cov.: 32

Gnomad AFR AF: 0.177

Gnomad AMI AF: 0.0428

Gnomad AMR AF: 0.0573

Gnomad ASJ AF: 0.0545

Gnomad EAS AF: 0.344

Gnomad SAS AF: 0.0710

Gnomad FIN AF: 0.105

Gnomad MID AF: 0.0791

Gnomad NFE AF: 0.0382

Gnomad OTH AF: 0.0851

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

GnomAD4 genome AF: 0.0952 AC: 14483 AN: 152200 Hom.: 1159 Cov.: 32 AF XY: 0.0986 AC XY: 7338 AN XY: 74410

African (AFR) AF: 0.177 AC: 7340 AN: 41514

American (AMR) AF: 0.0573 AC: 876 AN: 15278

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

East Asian (EAS) AF: 0.345 AC: 1784 AN: 5174

South Asian (SAS) AF: 0.0704 AC: 340 AN: 4830

European-Finnish (FIN) AF: 0.105 AC: 1119 AN: 10608

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

European-Non Finnish (NFE) AF: 0.0382 AC: 2595 AN: 68006

Other (OTH) AF: 0.0847 AC: 179 AN: 2114

Alfa AF: 0.0721 Hom.: 108

Bravo AF: 0.0965

Asia WGS AF: 0.199 AC: 692 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.92
CADD	Benign	1.4
DANN	Benign	0.26
PhyloP100		-0.055
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: rs9395950; hg19: chr6-54244192;