chr19-49062073-G-A
Variant names:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBS1BS2
The NM_006179.5(NTF4):c.-12-64C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00123 in 1,420,412 control chromosomes in the GnomAD database, including 20 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.0065 ( 9 hom., cov: 32)
Exomes 𝑓: 0.00059 ( 11 hom. )
Consequence
NTF4
NM_006179.5 intron
NM_006179.5 intron
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.678
Genes affected
NTF4 (HGNC:8024): (neurotrophin 4) This gene is a member of a family of neurotrophic factors, neurotrophins, that control survival and differentiation of mammalian neurons. The expression of this gene is ubiquitous and less influenced by environmental signals. While knock-outs of other neurotrophins including nerve growth factor, brain-derived neurotrophic factor, and neurotrophin 3 prove lethal during early postnatal development, NTF5-deficient mice only show minor cellular deficits and develop normally to adulthood. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -14 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.73).
BP6
Variant 19-49062073-G-A is Benign according to our data. Variant chr19-49062073-G-A is described in ClinVar as [Likely_benign]. Clinvar id is 1344980.Status of the report is criteria_provided_single_submitter, 1 stars.
BS1
Variant frequency is greater than expected in population afr. gnomad4 allele frequency = 0.00654 (997/152346) while in subpopulation AFR AF= 0.0229 (952/41566). AF 95% confidence interval is 0.0217. There are 9 homozygotes in gnomad4. There are 472 alleles in male gnomad4 subpopulation. Median coverage is 32. This position pass quality control queck.
BS2
High AC in GnomAd4 at 997 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTF4 | NM_006179.5 | c.-12-64C>T | intron_variant | Intron 1 of 1 | ENST00000593537.2 | NP_006170.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00652 AC: 992AN: 152228Hom.: 9 Cov.: 32
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GnomAD4 exome AF: 0.000592 AC: 751AN: 1268066Hom.: 11 AF XY: 0.000466 AC XY: 285AN XY: 611490
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GnomAD4 genome AF: 0.00654 AC: 997AN: 152346Hom.: 9 Cov.: 32 AF XY: 0.00634 AC XY: 472AN XY: 74502
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ClinVar
Significance: Likely benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not provided Benign:1
May 22, 2021
GeneDx
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
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Computational scores
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Name
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Prediction
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at