chr1-175320263-C-T

Position:

• chr1-175320263-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.*3094G>A variant causes a 3 prime UTR change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.24 in 152,072 control chromosomes in the GnomAD database, including 5,972 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 0.24 (5970 hom., cov: 32)
  • Exomes 𝑓: 0.13 (2 hom.)
• Consequence: TNR NM_003285.3 3_prime_UTR
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.110

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]

(HGNC:):

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.462 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
TNR	NM_003285.3	c.*3094G>A		3_prime_UTR_variant	23/23	ENST00000367674.7	NP_003276.3
LOC105371623	XR_001738299.2	n.92-719C>T		intron_variant, non_coding_transcript_variant
TNR	NM_001328635.2	c.*3094G>A		3_prime_UTR_variant	23/23		NP_001315564.1
LOC105371623	XR_001738302.2	n.92-719C>T		intron_variant, non_coding_transcript_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
TNR	ENST00000367674.7	c.*3094G>A		3_prime_UTR_variant	23/23	5	NM_003285.3	ENSP00000356646	P1
	ENST00000569593.1	n.196-719C>T		intron_variant, non_coding_transcript_variant		3

Frequencies

GnomAD3 genomes AF: 0.240 AC: 36369 AN: 151796 Hom.: 5945 Cov.: 32

Gnomad AFR AF: 0.468

Gnomad AMI AF: 0.228

Gnomad AMR AF: 0.166

Gnomad ASJ AF: 0.142

Gnomad EAS AF: 0.0338

Gnomad SAS AF: 0.0868

Gnomad FIN AF: 0.177

Gnomad MID AF: 0.149

Gnomad NFE AF: 0.160

Gnomad OTH AF: 0.213

GnomAD4 exome AF: 0.127 AC: 20 AN: 158 Hom.: 2 Cov.: 0 AF XY: 0.157 AC XY: 11 AN XY: 70

Gnomad4 AMR exome AF: 0.00

Gnomad4 FIN exome AF: 0.108

Gnomad4 NFE exome AF: 0.250

Gnomad4 OTH exome AF: 0.00

GnomAD4 genome AF: 0.240 AC: 36440 AN: 151914 Hom.: 5970 Cov.: 32 AF XY: 0.236 AC XY: 17501 AN XY: 74244

Gnomad4 AFR AF: 0.468

Gnomad4 AMR AF: 0.167

Gnomad4 ASJ AF: 0.142

Gnomad4 EAS AF: 0.0342

Gnomad4 SAS AF: 0.0859

Gnomad4 FIN AF: 0.177

Gnomad4 NFE AF: 0.160

Gnomad4 OTH AF: 0.213

Alfa AF: 0.170 Hom.: 3614

Bravo AF: 0.252

Asia WGS AF: 0.0880 AC: 305 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	9.3
DANN	Benign	0.64

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: rs875326; hg19: chr1-175289399;