rs12037583

chr1-175624169-C-T

Variant summary

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

The NM_003285.3(TNR):c.-164-95800G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0848 in 152,214 control chromosomes in the GnomAD database, including 922 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 0.085 (922 hom., cov: 32)
• Consequence: TNR NM_003285.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.0290

Genes affected

TNR (HGNC:11953): (tenascin R) This gene encodes a member of the tenascin family of extracellular matrix glycoproteins. The encoded protein is restricted to the central nervous system. The protein may play a role in neurite outgrowth, neural cell adhesion and modulation of sodium channel function. It is a constituent of perineuronal nets. [provided by RefSeq, Aug 2013]

ACMG classification

Verdict is Benign. Variant got -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 = 0.366 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
TNR	NM_003285.3	c.-164-95800G>A		intron_variant		ENST00000367674.7
TNR	NM_001328635.2	c.-1059-95800G>A		intron_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
TNR	ENST00000367674.7	c.-164-95800G>A		intron_variant		5	NM_003285.3	P1

Frequencies

GnomAD3 genomes AF: 0.0849 AC: 12914 AN: 152094 Hom.: 921 Cov.: 32

Gnomad AFR AF: 0.0180

Gnomad AMI AF: 0.0581

Gnomad AMR AF: 0.0700

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.380

Gnomad SAS AF: 0.146

Gnomad FIN AF: 0.108

Gnomad MID AF: 0.136

Gnomad NFE AF: 0.0960

Gnomad OTH AF: 0.0884

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

GnomAD4 genome AF: 0.0848 AC: 12909 AN: 152214 Hom.: 922 Cov.: 32 AF XY: 0.0881 AC XY: 6557 AN XY: 74422

Gnomad4 AFR AF: 0.0180

Gnomad4 AMR AF: 0.0702

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.380

Gnomad4 SAS AF: 0.146

Gnomad4 FIN AF: 0.108

Gnomad4 NFE AF: 0.0960

Gnomad4 OTH AF: 0.0880

Alfa AF: 0.0970 Hom.: 1082

Bravo AF: 0.0796

Asia WGS AF: 0.222 AC: 768 AN: 3476

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.90
Cadd	Benign	0.87
Dann	Benign	0.27

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: rs12037583; hg19: chr1-175593305;