4-182139833-C-A
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Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1
The XM_017008385.2(TENM3):c.-76+98090C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.419 in 152,070 control chromosomes in the GnomAD database, including 13,603 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 0.42 ( 13603 hom., cov: 34)
Consequence
TENM3
XM_017008385.2 intron
XM_017008385.2 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -1.35
Genes affected
TENM3 (HGNC:29944): (teneurin transmembrane protein 3) This gene encodes a member of the teneurin transmembrane protein family. The encoded protein may be involved in the regulation of neuronal development including development of the visual pathway. Mutations in this gene have been associated with microphthalmia and developmental dysplasia of the hip. [provided by RefSeq, Jan 2023]
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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=-0.88).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
TENM3 | XM_017008385.2 | c.-76+98090C>A | intron_variant | XP_016863874.1 | ||||
TENM3 | XM_047415933.1 | c.-76+98090C>A | intron_variant | XP_047271889.1 | ||||
TENM3 | XM_017008389.2 | c.-76+98090C>A | intron_variant | XP_016863878.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
TENM3-AS1 | ENST00000507869.6 | n.112+4214G>T | intron_variant | 2 | ||||||
TENM3-AS1 | ENST00000509012.5 | n.149+4214G>T | intron_variant | 4 |
Frequencies
GnomAD3 genomes AF: 0.419 AC: 63720AN: 151952Hom.: 13601 Cov.: 34
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We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.419 AC: 63743AN: 152070Hom.: 13603 Cov.: 34 AF XY: 0.416 AC XY: 30950AN XY: 74332
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ClinVar
Not reported inComputational scores
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Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at