rs3739670

Variant summary

Our verdict is Likely benign. Variant got -2 ACMG points: 2P and 4B. PM2BP4_Strong

The NM_018946.4(NANS):​c.102C>A​(p.Asp34Glu) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

Frequency

Genomes: not found (cov: 33)

Consequence

NANS
NM_018946.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -2.05
Variant links:
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 Likely_benign. Variant got -2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.028836131).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
NANSNM_018946.4 linkc.102C>A p.Asp34Glu missense_variant Exon 1 of 6 ENST00000210444.6 NP_061819.2
TRIM14XM_047424162.1 linkc.*29-21097G>T intron_variant Intron 6 of 6 XP_047280118.1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NANSENST00000210444.6 linkc.102C>A p.Asp34Glu missense_variant Exon 1 of 6 1 NM_018946.4 ENSP00000210444.5 Q9NR45
NANSENST00000480925.1 linkn.141C>A non_coding_transcript_exon_variant Exon 1 of 2 2
NANSENST00000495319.1 linkn.143C>A non_coding_transcript_exon_variant Exon 1 of 5 3

Frequencies

GnomAD3 genomes
Cov.:
33
GnomAD4 exome
Cov.:
39
GnomAD4 genome
Cov.:
33

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.089
BayesDel_addAF
Benign
-0.33
T
BayesDel_noAF
Benign
-0.71
CADD
Benign
0.73
DANN
Benign
0.89
DEOGEN2
Benign
0.00037
T
Eigen
Benign
-1.2
Eigen_PC
Benign
-1.1
FATHMM_MKL
Benign
0.41
N
LIST_S2
Benign
0.67
T
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.029
T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
-1.1
N
PrimateAI
Benign
0.44
T
PROVEAN
Benign
0.46
N
REVEL
Benign
0.069
Sift
Benign
1.0
T
Sift4G
Benign
1.0
T
Polyphen
0.0
B
Vest4
0.072
MutPred
0.27
Gain of MoRF binding (P = 0.1238);
MVP
0.15
MPC
0.20
ClinPred
0.20
T
GERP RS
-1.5
RBP_binding_hub_radar
0.92
RBP_regulation_power_radar
2.7
Varity_R
0.060
gMVP
0.31

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.0
Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs3739670; hg19: chr9-100819192; API