rs778317904

Variant summary

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

The NM_032592.4(ACCS):​c.110C>G​(p.Ser37Cys) 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: 32)

Consequence

ACCS
NM_032592.4 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.336
Variant links:
Genes affected
ACCS (HGNC:23989): (1-aminocyclopropane-1-carboxylate synthase homolog (inactive)) Enables identical protein binding activity. Predicted to be involved in biosynthetic process. [provided by Alliance of Genome Resources, Apr 2022]

Genome browser will be placed here

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=0.05622527).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
ACCSNM_032592.4 linkc.110C>G p.Ser37Cys missense_variant Exon 2 of 15 ENST00000263776.9 NP_115981.1 Q96QU6-1A0A0S2Z622

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
ACCSENST00000263776.9 linkc.110C>G p.Ser37Cys missense_variant Exon 2 of 15 1 NM_032592.4 ENSP00000263776.8 Q96QU6-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000398
AC:
1
AN:
251444
Hom.:
0
AF XY:
0.00
AC XY:
0
AN XY:
135910
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.00
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00000879
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
Cov.:
36
GnomAD4 genome
Cov.:
32
ExAC
AF:
0.00000824
AC:
1

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.076
BayesDel_addAF
Benign
-0.093
T
BayesDel_noAF
Benign
-0.37
CADD
Benign
13
DANN
Benign
0.79
DEOGEN2
Benign
0.028
T;T;.
Eigen
Benign
-0.66
Eigen_PC
Benign
-0.67
FATHMM_MKL
Benign
0.11
N
LIST_S2
Benign
0.59
T;T;T
M_CAP
Benign
0.010
T
MetaRNN
Benign
0.056
T;T;T
MetaSVM
Benign
-0.94
T
MutationAssessor
Benign
1.2
.;L;.
PrimateAI
Benign
0.27
T
PROVEAN
Benign
-0.89
N;N;N
REVEL
Benign
0.10
Sift
Benign
0.14
T;T;T
Sift4G
Benign
0.17
T;T;T
Polyphen
0.0040
.;B;.
Vest4
0.17
MutPred
0.13
Loss of phosphorylation at S37 (P = 0.0252);Loss of phosphorylation at S37 (P = 0.0252);Loss of phosphorylation at S37 (P = 0.0252);
MVP
0.45
MPC
0.088
ClinPred
0.055
T
GERP RS
2.5
Varity_R
0.072
gMVP
0.15

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: rs778317904; hg19: chr11-44089287; API