rs4237190
Positions:
Variant summary
Our verdict is Benign. Variant got -14 ACMG points: 0P and 14B. BP4_StrongBP6_ModerateBA1
The NM_018946.4(NANS):c.870+53A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.52 in 1,602,124 control chromosomes in the GnomAD database, including 225,964 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★).
Frequency
Genomes: 𝑓 0.61 ( 30828 hom., cov: 32)
Exomes 𝑓: 0.51 ( 195136 hom. )
Consequence
NANS
NM_018946.4 intron
NM_018946.4 intron
Scores
7
Clinical Significance
Conservation
PhyloP100: -0.326
Genes affected
NANS (HGNC:19237): (N-acetylneuraminate synthase) This gene encodes an enzyme that functions in the biosynthetic pathways of sialic acids. In vitro, the encoded protein uses N-acetylmannosamine 6-phosphate and mannose 6-phosphate as substrates to generate phosphorylated forms of N-acetylneuraminic acid (Neu5Ac) and 2-keto-3-deoxy-D-glycero-D-galacto-nononic acid (KDN), respectively; however, it exhibits much higher activity toward the Neu5Ac phosphate product. In insect cells, expression of this gene results in Neu5Ac and KDN production. This gene is related to the E. coli sialic acid synthase gene neuB, and it can partially restore sialic acid synthase activity in an E. coli neuB-negative mutant. [provided by RefSeq, Jul 2008]
TRIM14 (HGNC:16283): (tripartite motif containing 14) The protein encoded by this gene is a member of the tripartite motif (TRIM) family. The TRIM motif includes three zinc-binding domains, a RING, a B-box type 1 and a B-box type 2, and a coiled-coil region. The protein localizes to cytoplasmic bodies and its function has not been determined. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2010]
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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_addAF=-0.85618).
BP6
?
Variant 9-98081135-A-G is Benign according to our data. Variant chr9-98081135-A-G is described in ClinVar as [Benign]. Clinvar id is 1278431.Status of the report is criteria_provided_single_submitter, 1 stars.
BA1
?
GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.877 is higher than 0.05.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
NANS | NM_018946.4 | c.870+53A>G | intron_variant | ENST00000210444.6 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
NANS | ENST00000210444.6 | c.870+53A>G | intron_variant | 1 | NM_018946.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.608 AC: 92349AN: 152000Hom.: 30779 Cov.: 32
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GnomAD3 exomes AF: 0.544 AC: 133303AN: 244834Hom.: 38606 AF XY: 0.541 AC XY: 71581AN XY: 132350
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GnomAD4 exome AF: 0.511 AC: 740723AN: 1450006Hom.: 195136 Cov.: 35 AF XY: 0.513 AC XY: 369304AN XY: 719212
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GnomAD4 genome ? AF: 0.608 AC: 92458AN: 152118Hom.: 30828 Cov.: 32 AF XY: 0.602 AC XY: 44777AN XY: 74364
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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 | GeneDx | Nov 12, 2018 | - - |
Computational scores
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Name
Calibrated prediction
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BayesDel_addAF
Benign
T
BayesDel_noAF
Benign
CADD
Benign
DANN
Benign
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Benign
N
MutationTaster
Benign
P;P
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Splicing
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SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at