rs571803780
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Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 2P and 7B. PM2BP4_StrongBP6_ModerateBP7
The NM_001080477.4(TENM3):āc.5913T>Cā(p.Asp1971=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000991 in 1,614,000 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (ā ).
Frequency
Genomes: š 0.000026 ( 0 hom., cov: 33)
Exomes š: 0.0000082 ( 0 hom. )
Consequence
TENM3
NM_001080477.4 synonymous
NM_001080477.4 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.222
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 Likely_benign. Variant got -5 ACMG points.
PM2
?
Very rare variant in population databases, with high coverage;
BP4
?
Computational evidence support a benign effect (BayesDel_noAF=-0.56).
BP6
?
Variant 4-182792585-T-C is Benign according to our data. Variant chr4-182792585-T-C is described in ClinVar as [Likely_benign]. Clinvar id is 257354.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.222 with no splicing effect.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
TENM3 | NM_001080477.4 | c.5913T>C | p.Asp1971= | synonymous_variant | 26/28 | ENST00000511685.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
TENM3 | ENST00000511685.6 | c.5913T>C | p.Asp1971= | synonymous_variant | 26/28 | 5 | NM_001080477.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152180Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.0000120 AC: 3AN: 249232Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135208
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GnomAD4 exome AF: 0.00000821 AC: 12AN: 1461702Hom.: 0 Cov.: 33 AF XY: 0.0000124 AC XY: 9AN XY: 727132
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GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152298Hom.: 0 Cov.: 33 AF XY: 0.0000403 AC XY: 3AN XY: 74472
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
Likely benign, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | - | - - |
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