12-5494760-C-T
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Variant summary
Our verdict is Likely benign. Variant got -6 ACMG points: 0P and 6B. BP6_ModerateBS2
The NM_001102654.2(NTF3):c.585C>T(p.Gly195Gly) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000997 in 1,614,174 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 Benign (★).
Frequency
Genomes: 𝑓 0.00014 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000096 ( 0 hom. )
Consequence
NTF3
NM_001102654.2 synonymous
NM_001102654.2 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: -0.206
Genes affected
NTF3 (HGNC:8023): (neurotrophin 3) The protein encoded by this gene is a member of the neurotrophin family, that controls survival and differentiation of mammalian neurons. This protein is closely related to both nerve growth factor and brain-derived neurotrophic factor. It may be involved in the maintenance of the adult nervous system, and may affect development of neurons in the embryo when it is expressed in human placenta. NTF3-deficient mice generated by gene targeting display severe movement defects of the limbs. The mature peptide of this protein is identical in all mammals examined including human, pig, rat and mouse. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Likely_benign. Variant got -6 ACMG points.
BP6
Variant 12-5494760-C-T is Benign according to our data. Variant chr12-5494760-C-T is described in ClinVar as [Benign]. Clinvar id is 745236.Status of the report is criteria_provided_single_submitter, 1 stars.
BS2
High AC in GnomAd4 at 21 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTF3 | NM_001102654.2 | c.585C>T | p.Gly195Gly | synonymous_variant | 2/2 | ENST00000423158.4 | NP_001096124.1 | |
NTF3 | NM_002527.5 | c.546C>T | p.Gly182Gly | synonymous_variant | 1/1 | NP_002518.1 | ||
NTF3 | XM_011520963.3 | c.546C>T | p.Gly182Gly | synonymous_variant | 2/2 | XP_011519265.1 | ||
NTF3 | XM_047428901.1 | c.546C>T | p.Gly182Gly | synonymous_variant | 2/2 | XP_047284857.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
NTF3 | ENST00000423158.4 | c.585C>T | p.Gly195Gly | synonymous_variant | 2/2 | 1 | NM_001102654.2 | ENSP00000397297.2 | ||
NTF3 | ENST00000331010.7 | c.546C>T | p.Gly182Gly | synonymous_variant | 1/1 | 6 | ENSP00000328738.6 | |||
NTF3 | ENST00000535299.5 | n.232-11805C>T | intron_variant | 5 |
Frequencies
GnomAD3 genomes AF: 0.000138 AC: 21AN: 152166Hom.: 0 Cov.: 32
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GnomAD3 exomes AF: 0.000354 AC: 89AN: 251404Hom.: 0 AF XY: 0.000302 AC XY: 41AN XY: 135888
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GnomAD4 exome AF: 0.0000958 AC: 140AN: 1461890Hom.: 0 Cov.: 36 AF XY: 0.0000880 AC XY: 64AN XY: 727248
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GnomAD4 genome AF: 0.000138 AC: 21AN: 152284Hom.: 0 Cov.: 32 AF XY: 0.000201 AC XY: 15AN XY: 74454
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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 | Labcorp Genetics (formerly Invitae), Labcorp | May 24, 2018 | - - |
Computational scores
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BayesDel_noAF
Benign
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Benign
DANN
Benign
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SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: -2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at