chr4-182346995-C-CGG
Variant summary
Our verdict is Benign. Variant got -10 ACMG points: 0P and 10B. BP6_ModerateBA1
The NM_001080477.4(TENM3):c.511+73_511+74dup variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.212 in 813,618 control chromosomes in the GnomAD database, including 17,074 homozygotes. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.25 ( 5688 hom., cov: 0)
Exomes 𝑓: 0.20 ( 11386 hom. )
Consequence
TENM3
NM_001080477.4 intron
NM_001080477.4 intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 0.190
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 -10 ACMG points.
BP6
?
Variant 4-182346995-C-CGG is Benign according to our data. Variant chr4-182346995-C-CGG is described in ClinVar as [Benign]. Clinvar id is 1282190.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.332 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM3 | NM_001080477.4 | c.511+73_511+74dup | intron_variant | ENST00000511685.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM3 | ENST00000511685.6 | c.511+73_511+74dup | intron_variant | 5 | NM_001080477.4 | P1 | |||
TENM3 | ENST00000513201.1 | n.761+73_761+74dup | intron_variant, non_coding_transcript_variant | 1 |
Frequencies
GnomAD3 genomes ? AF: 0.250 AC: 37072AN: 148502Hom.: 5689 Cov.: 0
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GnomAD4 exome AF: 0.204 AC: 135404AN: 665010Hom.: 11386 AF XY: 0.204 AC XY: 67433AN XY: 329886
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GnomAD4 genome ? AF: 0.249 AC: 37061AN: 148608Hom.: 5688 Cov.: 0 AF XY: 0.247 AC XY: 17829AN XY: 72168
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
Benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 04, 2018 | - - |
Computational scores
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Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at