rs371445287

Variant summary

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

The NM_001088.3(AANAT):​c.487G>A​(p.Ala163Thr) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000174 in 1,605,052 control chromosomes in the GnomAD database, with no homozygous occurrence. 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: 𝑓 0.000013 ( 0 hom., cov: 32)
Exomes 𝑓: 0.000018 ( 0 hom. )

Consequence

AANAT
NM_001088.3 missense

Scores

19

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.0360
Variant links:
Genes affected
AANAT (HGNC:19): (aralkylamine N-acetyltransferase) The protein encoded by this gene belongs to the acetyltransferase superfamily. It is the penultimate enzyme in melatonin synthesis and controls the night/day rhythm in melatonin production in the vertebrate pineal gland. Melatonin is essential for the function of the circadian clock that influences activity and sleep. This enzyme is regulated by cAMP-dependent phosphorylation that promotes its interaction with 14-3-3 proteins and thus protects the enzyme against proteasomal degradation. This gene may contribute to numerous genetic diseases such as delayed sleep phase syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2009]

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=0.0538325).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt
AANATNM_001088.3 linkc.487G>A p.Ala163Thr missense_variant Exon 4 of 4 ENST00000392492.8 NP_001079.1 Q16613-1F1T0I5
AANATNM_001166579.2 linkc.622G>A p.Ala208Thr missense_variant Exon 7 of 7 NP_001160051.1 Q16613-2
AANATNR_110548.2 linkn.743G>A non_coding_transcript_exon_variant Exon 4 of 4

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
AANATENST00000392492.8 linkc.487G>A p.Ala163Thr missense_variant Exon 4 of 4 1 NM_001088.3 ENSP00000376282.2 Q16613-1
AANATENST00000250615.7 linkc.622G>A p.Ala208Thr missense_variant Exon 7 of 7 1 ENSP00000250615.2 Q16613-2
AANATENST00000587798.1 linkn.*264G>A non_coding_transcript_exon_variant Exon 4 of 4 5 ENSP00000468239.1 K7ERF6
AANATENST00000587798.1 linkn.*264G>A 3_prime_UTR_variant Exon 4 of 4 5 ENSP00000468239.1 K7ERF6

Frequencies

GnomAD3 genomes
AF:
0.0000131
AC:
2
AN:
152244
Hom.:
0
Cov.:
32
show subpopulations
Gnomad AFR
AF:
0.0000241
Gnomad AMI
AF:
0.00
Gnomad AMR
AF:
0.00
Gnomad ASJ
AF:
0.00
Gnomad EAS
AF:
0.000192
Gnomad SAS
AF:
0.00
Gnomad FIN
AF:
0.00
Gnomad MID
AF:
0.00
Gnomad NFE
AF:
0.00
Gnomad OTH
AF:
0.00
GnomAD3 exomes
AF:
0.0000217
AC:
5
AN:
230802
Hom.:
0
AF XY:
0.0000238
AC XY:
3
AN XY:
125934
show subpopulations
Gnomad AFR exome
AF:
0.0000704
Gnomad AMR exome
AF:
0.0000303
Gnomad ASJ exome
AF:
0.00
Gnomad EAS exome
AF:
0.0000581
Gnomad SAS exome
AF:
0.0000696
Gnomad FIN exome
AF:
0.00
Gnomad NFE exome
AF:
0.00
Gnomad OTH exome
AF:
0.00
GnomAD4 exome
AF:
0.0000179
AC:
26
AN:
1452690
Hom.:
0
Cov.:
31
AF XY:
0.0000138
AC XY:
10
AN XY:
722042
show subpopulations
Gnomad4 AFR exome
AF:
0.00
Gnomad4 AMR exome
AF:
0.0000229
Gnomad4 ASJ exome
AF:
0.00
Gnomad4 EAS exome
AF:
0.00
Gnomad4 SAS exome
AF:
0.0000590
Gnomad4 FIN exome
AF:
0.00
Gnomad4 NFE exome
AF:
0.0000162
Gnomad4 OTH exome
AF:
0.0000334
GnomAD4 genome
AF:
0.0000131
AC:
2
AN:
152362
Hom.:
0
Cov.:
32
AF XY:
0.0000134
AC XY:
1
AN XY:
74508
show subpopulations
Gnomad4 AFR
AF:
0.0000240
Gnomad4 AMR
AF:
0.00
Gnomad4 ASJ
AF:
0.00
Gnomad4 EAS
AF:
0.000193
Gnomad4 SAS
AF:
0.00
Gnomad4 FIN
AF:
0.00
Gnomad4 NFE
AF:
0.00
Gnomad4 OTH
AF:
0.00
Bravo
AF:
0.0000113
ESP6500AA
AF:
0.000227
AC:
1
ESP6500EA
AF:
0.00
AC:
0
ExAC
AF:
0.0000165
AC:
2

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
AlphaMissense
Benign
0.071
BayesDel_addAF
Benign
-0.52
T
BayesDel_noAF
Benign
-0.80
CADD
Benign
0.028
DANN
Benign
0.91
DEOGEN2
Benign
0.14
.;T
Eigen
Benign
-1.3
Eigen_PC
Benign
-1.4
FATHMM_MKL
Benign
0.098
N
LIST_S2
Benign
0.66
T;T
M_CAP
Benign
0.0053
T
MetaRNN
Benign
0.054
T;T
MetaSVM
Benign
-0.95
T
MutationAssessor
Benign
1.6
.;L
PrimateAI
Benign
0.25
T
PROVEAN
Benign
-0.25
N;N
REVEL
Benign
0.033
Sift
Benign
0.40
T;T
Sift4G
Benign
0.41
T;T
Polyphen
0.0010
.;B
Vest4
0.029
MVP
0.085
MPC
0.055
ClinPred
0.026
T
GERP RS
-5.7
Varity_R
0.056
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: rs371445287; hg19: chr17-74465915; COSMIC: COSV51684404; COSMIC: COSV51684404; API