chr17-9022892-C-T
Variant names:
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 0P and 9B. BP4_ModerateBP6_ModerateBP7BS2
The NM_004822.3(NTN1):c.519C>T(p.Pro173Pro) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000202 in 1,612,312 control chromosomes in the GnomAD database, including 2 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★).
Frequency
Genomes: 𝑓 0.00023 ( 0 hom., cov: 33)
Exomes 𝑓: 0.00020 ( 2 hom. )
Consequence
NTN1
NM_004822.3 synonymous
NM_004822.3 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.126
Genes affected
NTN1 (HGNC:8029): (netrin 1) Netrin is included in a family of laminin-related secreted proteins. The function of this gene has not yet been defined; however, netrin is thought to be involved in axon guidance and cell migration during development. Mutations and loss of expression of netrin suggest that variation in netrin may be involved in cancer development. [provided by RefSeq, Jul 2008]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -9 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.45).
BP6
Variant 17-9022892-C-T is Benign according to our data. Variant chr17-9022892-C-T is described in ClinVar as [Likely_benign]. Clinvar id is 2647463.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.126 with no splicing effect.
BS2
High AC in GnomAd4 at 35 AD gene.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
NTN1 | NM_004822.3 | c.519C>T | p.Pro173Pro | synonymous_variant | Exon 2 of 7 | ENST00000173229.7 | NP_004813.2 | |
NTN1 | XM_006721595.4 | c.519C>T | p.Pro173Pro | synonymous_variant | Exon 2 of 7 | XP_006721658.1 | ||
NTN1 | XM_047437096.1 | c.519C>T | p.Pro173Pro | synonymous_variant | Exon 2 of 7 | XP_047293052.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000230 AC: 35AN: 151990Hom.: 0 Cov.: 33
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GnomAD3 exomes AF: 0.000376 AC: 91AN: 241898Hom.: 2 AF XY: 0.000370 AC XY: 49AN XY: 132602
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GnomAD4 exome AF: 0.000199 AC: 290AN: 1460204Hom.: 2 Cov.: 32 AF XY: 0.000183 AC XY: 133AN XY: 726354
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GnomAD4 genome AF: 0.000230 AC: 35AN: 152108Hom.: 0 Cov.: 33 AF XY: 0.000323 AC XY: 24AN XY: 74354
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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
Jul 01, 2023
CeGaT Center for Human Genetics Tuebingen
Significance: Likely benign
Review Status: criteria provided, single submitter
Collection Method: clinical testing
NTN1: BP4 -
Computational scores
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Name
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BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Splicing
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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at