1-175320263-C-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

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

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.110
Variant links:
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]

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ACMG classification

Classification made for transcript

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
TNRNM_003285.3 linkuse as main transcriptc.*3094G>A 3_prime_UTR_variant 23/23 ENST00000367674.7 NP_003276.3
LOC105371623XR_001738299.2 linkuse as main transcriptn.92-719C>T intron_variant, non_coding_transcript_variant
TNRNM_001328635.2 linkuse as main transcriptc.*3094G>A 3_prime_UTR_variant 23/23 NP_001315564.1
LOC105371623XR_001738302.2 linkuse as main transcriptn.92-719C>T intron_variant, non_coding_transcript_variant

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Protein Appris UniProt
TNRENST00000367674.7 linkuse as main transcriptc.*3094G>A 3_prime_UTR_variant 23/235 NM_003285.3 ENSP00000356646 P1Q92752-1
ENST00000569593.1 linkuse as main transcriptn.196-719C>T intron_variant, non_coding_transcript_variant 3

Frequencies

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

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs875326; hg19: chr1-175289399; API