chr1-175330113-G-A
Variant summary
Our verdict is Benign. Variant got -21 ACMG points: 0P and 21B. BP4_StrongBP6_Very_StrongBP7BS1BS2
The NM_003285.3(TNR):c.3754C>T(p.Leu1252=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00327 in 1,611,056 control chromosomes in the GnomAD database, including 22 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).
Frequency
Genomes: 𝑓 0.0025 ( 2 hom., cov: 33)
Exomes 𝑓: 0.0034 ( 20 hom. )
Consequence
TNR
NM_003285.3 synonymous
NM_003285.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 2.38
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 -21 ACMG points.
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.48).
BP6
?
Variant 1-175330113-G-A is Benign according to our data. Variant chr1-175330113-G-A is described in ClinVar as [Benign]. Clinvar id is 708860.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr1-175330113-G-A is described in Lovd as [Benign].
BP7
?
Synonymous conserved (PhyloP=2.38 with no splicing effect.
BS1
?
Variant frequency is greater than expected in population nfe. gnomad4 allele frequency = 0.00247 (377/152372) while in subpopulation NFE AF= 0.00341 (232/68032). AF 95% confidence interval is 0.00305. There are 2 homozygotes in gnomad4. There are 151 alleles in male gnomad4 subpopulation. Median coverage is 33. This position pass quality control queck.
BS2
?
High AC in GnomAd at 377 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TNR | NM_003285.3 | c.3754C>T | p.Leu1252= | synonymous_variant | 21/23 | ENST00000367674.7 | |
LOC105371623 | XR_001738299.2 | n.318+603G>A | intron_variant, non_coding_transcript_variant | ||||
TNR | NM_001328635.2 | c.2755C>T | p.Leu919= | synonymous_variant | 21/23 | ||
LOC105371623 | XR_001738302.2 | n.232-3209G>A | intron_variant, non_coding_transcript_variant |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TNR | ENST00000367674.7 | c.3754C>T | p.Leu1252= | synonymous_variant | 21/23 | 5 | NM_003285.3 | P1 | |
ENST00000569593.1 | n.336-264G>A | intron_variant, non_coding_transcript_variant | 3 |
Frequencies
GnomAD3 genomes ? AF: 0.00248 AC: 377AN: 152254Hom.: 2 Cov.: 33
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GnomAD3 exomes AF: 0.00313 AC: 784AN: 250556Hom.: 2 AF XY: 0.00300 AC XY: 406AN XY: 135380
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GnomAD4 exome AF: 0.00336 AC: 4894AN: 1458684Hom.: 20 Cov.: 29 AF XY: 0.00325 AC XY: 2353AN XY: 725016
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ClinVar
Significance: Benign
Submissions summary: Benign:2
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Benign:2
Benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2024 | TNR: BP4, BS1, BS2 - |
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 31, 2019 | - - |
Computational scores
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BayesDel_noAF
Benign
Cadd
Benign
Dann
Benign
Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at