chr11-77842549-G-C

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2BP4

The NM_024684.4(AAMDC):ā€‹c.53G>Cā€‹(p.Gly18Ala) variant causes a missense change. The variant allele was found at a frequency of 0.000512 in 1,614,000 control chromosomes in the GnomAD database, including 1 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (ā˜…).

Frequency

Genomes: š‘“ 0.00031 ( 0 hom., cov: 32)
Exomes š‘“: 0.00053 ( 1 hom. )

Consequence

AAMDC
NM_024684.4 missense

Scores

2
12
5

Clinical Significance

Uncertain significance criteria provided, single submitter U:1

Conservation

PhyloP100: 6.61
Variant links:
Genes affected
AAMDC (HGNC:30205): (adipogenesis associated Mth938 domain containing) Predicted to be involved in positive regulation of fat cell differentiation. Predicted to act upstream of or within negative regulation of apoptotic process and positive regulation of transcription by RNA polymerase II. Predicted to be active in cytoplasm. [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 1 ACMG points.

PM2
Very rare variant in population databases, with high coverage;
BP4
Computational evidence support a benign effect (MetaRNN=0.2949015).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
AAMDCNM_024684.4 linkuse as main transcriptc.53G>C p.Gly18Ala missense_variant 2/4 ENST00000393427.7

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
AAMDCENST00000393427.7 linkuse as main transcriptc.53G>C p.Gly18Ala missense_variant 2/41 NM_024684.4 P1Q9H7C9-1
ENST00000525594.1 linkuse as main transcriptn.112-12422C>G intron_variant, non_coding_transcript_variant 4

Frequencies

GnomAD3 genomes
AF:
0.000309
AC:
47
AN:
152120
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.000169
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.000458
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.00
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.000485
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.000338
AC:
85
AN:
251134
Hom.:
0
AF XY:
0.000346
AC XY:
47
AN XY:
135734
show subpopulations
Gnomad AFR exome
AF:
0.000185
Gnomad AMR exome
AF:
0.000463
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.00
Gnomad SAS exome
AF:
0.00
Gnomad FIN exome
AF:
0.0000462
Gnomad NFE exome
AF:
0.000555
Gnomad OTH exome
AF:
0.000327
GnomAD4 exome
AF:
0.000533
AC:
779
AN:
1461762
Hom.:
1
Cov.:
30
AF XY:
0.000531
AC XY:
386
AN XY:
727170
show subpopulations
Gnomad4 AFR exome
AF:
0.0000597
Gnomad4 AMR exome
AF:
0.000470
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.00
Gnomad4 FIN exome
AF:
0.0000187
Gnomad4 NFE exome
AF:
0.000668
Gnomad4 OTH exome
AF:
0.000199
GnomAD4 genome
AF:
0.000309
AC:
47
AN:
152238
Hom.:
0
Cov.:
32
AF XY:
0.000255
AC XY:
19
AN XY:
74404
show subpopulations
Gnomad4 AFR
AF:
0.000169
Gnomad4 AMR
AF:
0.000458
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.00
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.000485
Gnomad4 OTH
AF:
0.00
Alfa
AF:
0.000463
Hom.:
0
Bravo
AF:
0.000397
TwinsUK
AF:
0.00
AC:
0
ALSPAC
AF:
0.000778
AC:
3
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.000466
AC:
4
ExAC
AF:
0.000239
AC:
29
EpiCase
AF:
0.000491
EpiControl
AF:
0.000771

ClinVar

Significance: Uncertain significance
Submissions summary: Uncertain:1
Revision: criteria provided, single submitter
LINK: link

Submissions by phenotype

not specified Uncertain:1
Uncertain significance, criteria provided, single submitterclinical testingAmbry GeneticsMay 05, 2023The c.53G>C (p.G18A) alteration is located in exon 2 (coding exon 1) of the AAMDC gene. This alteration results from a G to C substitution at nucleotide position 53, causing the glycine (G) at amino acid position 18 to be replaced by an alanine (A). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.19
BayesDel_addAF
Benign
-0.053
T
BayesDel_noAF
Uncertain
0.040
CADD
Uncertain
24
DANN
Uncertain
1.0
DEOGEN2
Uncertain
0.67
.;D;D;.;.;.;T;T;D
Eigen
Pathogenic
0.71
Eigen_PC
Pathogenic
0.72
FATHMM_MKL
Uncertain
0.87
D
LIST_S2
Uncertain
0.95
D;.;D;D;.;D;D;D;D
M_CAP
Benign
0.020
T
MetaRNN
Benign
0.29
T;T;T;T;T;T;T;T;T
MetaSVM
Uncertain
0.11
D
MutationAssessor
Uncertain
2.7
M;M;M;.;.;.;.;.;.
MutationTaster
Benign
1.0
D;D;D;D;D;D;D;D
PrimateAI
Uncertain
0.59
T
PROVEAN
Uncertain
-2.7
D;D;D;D;D;.;D;N;D
REVEL
Uncertain
0.46
Sift
Uncertain
0.016
D;D;D;D;D;.;D;D;D
Sift4G
Uncertain
0.018
D;T;T;D;D;D;D;D;T
Polyphen
0.99
D;P;P;D;.;.;.;.;.
Vest4
0.61
MVP
0.64
MPC
0.074
ClinPred
0.26
T
GERP RS
4.7
Varity_R
0.70
gMVP
0.74

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: rs138381967; hg19: chr11-77553595; API