11-58710137-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2

The NM_201648.3(GLYAT):​c.520G>A​(p.Asp174Asn) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000684 in 1,461,466 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts 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. D174H) has been classified as Uncertain significance.

Frequency

Genomes: not found (cov: 32)
Exomes 𝑓: 6.8e-7 ( 0 hom. )

Consequence

GLYAT
NM_201648.3 missense

Scores

3
16

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 0.443
Variant links:
Genes affected
GLYAT (HGNC:13734): (glycine-N-acyltransferase) The glycine-N-acyltransferase protein conjugates glycine with acyl-CoA substrates in the mitochondria. The protein is thought to be important in the detoxification of endogenous and xenobiotic acyl-CoA's. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]

Genome browser will be placed here

ACMG classification

Classification made for transcript

Verdict is Uncertain_significance. Variant got 2 ACMG points.

PM2
Very rare variant in population databases, with high coverage;

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
GLYATNM_201648.3 linkc.520G>A p.Asp174Asn missense_variant Exon 6 of 6 ENST00000344743.8 NP_964011.2 Q6IB77-1A0A384P5E3
GLYATXM_017017087.1 linkc.328G>A p.Asp110Asn missense_variant Exon 6 of 6 XP_016872576.1
GLYATNM_005838.4 linkc.*449G>A 3_prime_UTR_variant Exon 5 of 5 NP_005829.3 Q6IB77-2

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
GLYATENST00000344743.8 linkc.520G>A p.Asp174Asn missense_variant Exon 6 of 6 1 NM_201648.3 ENSP00000340200.3 Q6IB77-1

Frequencies

GnomAD3 genomes
Cov.:
32
GnomAD3 exomes
AF:
0.00000799
AC:
2
AN:
250422
Hom.:
0
AF XY:
0.00000739
AC XY:
1
AN XY:
135294
show subpopulations
Gnomad AFR exome
AF:
0.00
Gnomad AMR exome
AF:
0.0000290
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:
0.00000885
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
6.84e-7
AC:
1
AN:
1461466
Hom.:
0
Cov.:
32
AF XY:
0.00
AC XY:
0
AN XY:
726998
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000224
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.:
32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.11
BayesDel_addAF
Benign
-0.42
T
BayesDel_noAF
Benign
-0.75
CADD
Benign
17
DANN
Uncertain
1.0
DEOGEN2
Benign
0.11
T;T;T
Eigen
Benign
-0.40
Eigen_PC
Benign
-0.50
FATHMM_MKL
Benign
0.052
N
LIST_S2
Benign
0.78
T;.;.
M_CAP
Benign
0.014
T
MetaRNN
Benign
0.39
T;T;T
MetaSVM
Benign
-1.0
T
MutationAssessor
Uncertain
2.5
M;M;M
PrimateAI
Benign
0.36
T
PROVEAN
Uncertain
-3.7
.;D;D
REVEL
Benign
0.13
Sift
Benign
0.072
.;T;T
Sift4G
Benign
0.14
T;T;T
Polyphen
0.28
B;B;B
Vest4
0.10
MutPred
0.79
Gain of MoRF binding (P = 0.0822);Gain of MoRF binding (P = 0.0822);Gain of MoRF binding (P = 0.0822);
MVP
0.38
MPC
0.064
ClinPred
0.42
T
GERP RS
2.5
Varity_R
0.10
gMVP
0.25

Splicing

Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
0.22
Details are displayed if max score is > 0.2
DS_AL_spliceai
0.22
Position offset: 31

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: rs376065098; hg19: chr11-58477610; API