NM_001330449.2:c.31C>A

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_001330449.2(AMDHD2):​c.31C>A​(p.Arg11Ser) 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. 13/20 in silico tools predict a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R11C) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 29)
Exomes 𝑓: 0.0 ( 0 hom. )
Failed GnomAD Quality Control

Consequence

AMDHD2
NM_001330449.2 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.972
Variant links:
Genes affected
AMDHD2 (HGNC:24262): (amidohydrolase domain containing 2) Enables N-acetylglucosamine-6-phosphate deacetylase activity. Predicted to be involved in N-acetylglucosamine catabolic process. Located in nucleus. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 0 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.14429826).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AMDHD2NM_001330449.2 linkc.31C>A p.Arg11Ser missense_variant Exon 1 of 11 ENST00000293971.11 NP_001317378.1 Q9Y303-1

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AMDHD2ENST00000293971.11 linkc.31C>A p.Arg11Ser missense_variant Exon 1 of 11 1 NM_001330449.2 ENSP00000293971.6 Q9Y303-1
ENSG00000259784ENST00000569317.1 linkc.80-495C>A intron_variant Intron 1 of 3 3 ENSP00000455561.1 H3BQ15

Frequencies

GnomAD3 genomes
Cov.:
29
GnomAD4 exome
Data not reliable, filtered out with message: AC0
AF:
0.00
AC:
0
AN:
1078912
Hom.:
0
Cov.:
31
AF XY:
0.00
AC XY:
0
AN XY:
509946
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.00
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.00
Gnomad4 OTH exome
AF:
0.00
GnomAD4 genome
Cov.:
29

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.15
BayesDel_addAF
Benign
-0.072
T
BayesDel_noAF
Benign
-0.34
CADD
Benign
16
DANN
Benign
0.83
DEOGEN2
Benign
0.086
T;.;.;.;.;T;T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.3
FATHMM_MKL
Pathogenic
1.0
D
LIST_S2
Benign
0.68
T;T;T;T;T;T;T
M_CAP
Pathogenic
0.45
D
MetaRNN
Benign
0.14
T;T;T;T;T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Benign
0.81
L;L;L;.;.;.;.
PrimateAI
Pathogenic
0.85
D
PROVEAN
Benign
-0.45
N;N;N;.;N;N;N
REVEL
Benign
0.057
Sift
Benign
0.61
T;T;D;.;T;T;T
Sift4G
Benign
0.38
T;T;D;.;T;T;T
Polyphen
0.0
B;B;B;.;.;.;.
Vest4
0.18
MutPred
0.62
Loss of MoRF binding (P = 0.0115);Loss of MoRF binding (P = 0.0115);Loss of MoRF binding (P = 0.0115);Loss of MoRF binding (P = 0.0115);Loss of MoRF binding (P = 0.0115);Loss of MoRF binding (P = 0.0115);Loss of MoRF binding (P = 0.0115);
MVP
0.081
MPC
0.81
ClinPred
0.54
D
GERP RS
0.46
RBP_binding_hub_radar
0.0
RBP_regulation_power_radar
1.0
Varity_R
0.081
gMVP
0.50

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: rs761700526; hg19: chr16-2570490; API