rs61731573
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Variant summary
Our verdict is Benign. Variant got -13 ACMG points: 0P and 13B. BP4_ModerateBP6_ModerateBP7BA1
The NM_004558.5(NRTN):c.144C>T(p.Asp48=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00415 in 1,606,660 control chromosomes in the GnomAD database, including 247 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.023 ( 137 hom., cov: 33)
Exomes 𝑓: 0.0022 ( 110 hom. )
Consequence
NRTN
NM_004558.5 synonymous
NM_004558.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.179
Genes affected
NRTN (HGNC:8007): (neurturin) This gene encodes a secreted ligand of the TGF-beta (transforming growth factor-beta) superfamily of proteins. The encoded preproprotein is proteolytically processed to generate the mature protein. This protein signals through the RET receptor tyrosine kinase and a GPI-linked coreceptor, and promotes survival of neuronal populations. A neurturin mutation has been described in a family with Hirschsprung Disease. [provided by RefSeq, Aug 2016]
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ACMG classification
Classification made for transcript
Verdict is Benign. Variant got -13 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.39).
BP6
Variant 19-5824309-C-T is Benign according to our data. Variant chr19-5824309-C-T is described in ClinVar as [Benign]. Clinvar id is 259425.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
Synonymous conserved (PhyloP=0.179 with no splicing effect.
BA1
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.0779 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRTN | NM_004558.5 | c.144C>T | p.Asp48= | synonymous_variant | 2/3 | ENST00000303212.3 | |
NRTN | XM_047438890.1 | c.144C>T | p.Asp48= | synonymous_variant | 1/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRTN | ENST00000303212.3 | c.144C>T | p.Asp48= | synonymous_variant | 2/3 | 1 | NM_004558.5 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0230 AC: 3502AN: 152184Hom.: 137 Cov.: 33
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GnomAD3 exomes AF: 0.00597 AC: 1393AN: 233450Hom.: 45 AF XY: 0.00454 AC XY: 578AN XY: 127206
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GnomAD4 exome AF: 0.00218 AC: 3166AN: 1454358Hom.: 110 Cov.: 31 AF XY: 0.00182 AC XY: 1316AN XY: 723262
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GnomAD4 genome AF: 0.0230 AC: 3504AN: 152302Hom.: 137 Cov.: 33 AF XY: 0.0222 AC XY: 1653AN XY: 74476
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ClinVar
Significance: Benign
Submissions summary: Benign:1
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
not specified Benign:1
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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Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at