chr6-54317505-T-C

Position:

• chr6-54317505-T-C

Variant summary

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

The NM_014464.4(TINAG):​c.356-3074T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.608 in 151,962 control chromosomes in the GnomAD database, including 28,992 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 0.61 (28992 hom., cov: 31)
• Consequence: TINAG NM_014464.4 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.452

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=-0.94).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TINAG	NM_014464.4	c.356-3074T>C		intron_variant		ENST00000259782.9

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TINAG	ENST00000259782.9	c.356-3074T>C		intron_variant		1	NM_014464.4	P1
TINAG	ENST00000370864.3	c.302-3074T>C		intron_variant		2
TINAG	ENST00000370869.7	c.344-3074T>C		intron_variant		3
TINAG	ENST00000486436.1	n.418-3074T>C		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.608 AC: 92268 AN: 151842 Hom.: 28978 Cov.: 31

Gnomad AFR AF: 0.453

Gnomad AMI AF: 0.510

Gnomad AMR AF: 0.571

Gnomad ASJ AF: 0.771

Gnomad EAS AF: 0.754

Gnomad SAS AF: 0.559

Gnomad FIN AF: 0.701

Gnomad MID AF: 0.747

Gnomad NFE AF: 0.678

Gnomad OTH AF: 0.645

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

GnomAD4 genome AF: 0.608 AC: 92321 AN: 151962 Hom.: 28992 Cov.: 31 AF XY: 0.609 AC XY: 45236 AN XY: 74268

Gnomad4 AFR AF: 0.454

Gnomad4 AMR AF: 0.571

Gnomad4 ASJ AF: 0.771

Gnomad4 EAS AF: 0.754

Gnomad4 SAS AF: 0.561

Gnomad4 FIN AF: 0.701

Gnomad4 NFE AF: 0.678

Gnomad4 OTH AF: 0.645

Alfa AF: 0.630 Hom.: 4860

Bravo AF: 0.592

Asia WGS AF: 0.633 AC: 2199 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	0.41
DANN	Benign	0.56

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: rs6909083; hg19: chr6-54182303;