rs7255720
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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):āc.474G>Cā(p.Arg158=) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0517 in 1,427,226 control chromosomes in the GnomAD database, including 2,535 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (ā ).
Frequency
Genomes: š 0.071 ( 520 hom., cov: 32)
Exomes š: 0.049 ( 2015 hom. )
Consequence
NRTN
NM_004558.5 synonymous
NM_004558.5 synonymous
Scores
2
Clinical Significance
Conservation
PhyloP100: 0.601
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 19-5828053-G-C is Benign according to our data. Variant chr19-5828053-G-C is described in ClinVar as [Benign]. Clinvar id is 259428.Status of the report is criteria_provided_single_submitter, 1 stars.
BP7
?
Synonymous conserved (PhyloP=0.601 with no splicing effect.
BA1
?
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.128 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NRTN | NM_004558.5 | c.474G>C | p.Arg158= | synonymous_variant | 3/3 | ENST00000303212.3 | |
NRTN | XM_047438890.1 | c.474G>C | p.Arg158= | synonymous_variant | 2/2 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NRTN | ENST00000303212.3 | c.474G>C | p.Arg158= | synonymous_variant | 3/3 | 1 | NM_004558.5 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0707 AC: 10658AN: 150716Hom.: 520 Cov.: 32
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GnomAD3 exomes AF: 0.0503 AC: 2492AN: 49592Hom.: 88 AF XY: 0.0570 AC XY: 1673AN XY: 29328
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GnomAD4 exome AF: 0.0494 AC: 63114AN: 1276404Hom.: 2015 Cov.: 33 AF XY: 0.0513 AC XY: 32187AN XY: 627342
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GnomAD4 genome ? AF: 0.0708 AC: 10685AN: 150822Hom.: 520 Cov.: 32 AF XY: 0.0715 AC XY: 5260AN XY: 73596
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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