chr11-71456989-A-G
Variant names:
Variant summary
Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_StrongBA1
The NM_018161.5(NADSYN1):c.147-1439A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.61 in 152,134 control chromosomes in the GnomAD database, including 29,921 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Genomes: 𝑓 0.61 ( 29921 hom., cov: 34)
Consequence
NADSYN1
NM_018161.5 intron
NM_018161.5 intron
Scores
2
Clinical Significance
Not reported in ClinVar
Conservation
PhyloP100: -0.398
Publications
23 publications found
Genes affected
NADSYN1 (HGNC:29832): (NAD synthetase 1) Nicotinamide adenine dinucleotide (NAD) is a coenzyme in metabolic redox reactions, a precursor for several cell signaling molecules, and a substrate for protein posttranslational modifications. NAD synthetase (EC 6.3.5.1) catalyzes the final step in the biosynthesis of NAD from nicotinic acid adenine dinucleotide (NaAD).[supplied by OMIM, Apr 2004]
NADSYN1 Gene-Disease associations (from GenCC):
- vertebral, cardiac, renal, and limb defects syndrome 3Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
- congenital vertebral-cardiac-renal anomalies syndromeInheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet
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ACMG classification
Classification was made for transcript
Our verdict: Benign. The variant received -12 ACMG points.
BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.93).
BA1
GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.739 is higher than 0.05.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes AF: 0.610 AC: 92673AN: 152014Hom.: 29878 Cov.: 34 show subpopulations
GnomAD3 genomes
AF:
AC:
92673
AN:
152014
Hom.:
Cov.:
34
Gnomad AFR
AF:
Gnomad AMI
AF:
Gnomad AMR
AF:
Gnomad ASJ
AF:
Gnomad EAS
AF:
Gnomad SAS
AF:
Gnomad FIN
AF:
Gnomad MID
AF:
Gnomad NFE
AF:
Gnomad OTH
AF:
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome AF: 0.610 AC: 92764AN: 152134Hom.: 29921 Cov.: 34 AF XY: 0.592 AC XY: 44046AN XY: 74390 show subpopulations
GnomAD4 genome
AF:
AC:
92764
AN:
152134
Hom.:
Cov.:
34
AF XY:
AC XY:
44046
AN XY:
74390
show subpopulations
African (AFR)
AF:
AC:
21006
AN:
41500
American (AMR)
AF:
AC:
7828
AN:
15296
Ashkenazi Jewish (ASJ)
AF:
AC:
2134
AN:
3472
East Asian (EAS)
AF:
AC:
1960
AN:
5138
South Asian (SAS)
AF:
AC:
1023
AN:
4828
European-Finnish (FIN)
AF:
AC:
6237
AN:
10596
Middle Eastern (MID)
AF:
AC:
139
AN:
292
European-Non Finnish (NFE)
AF:
AC:
50606
AN:
67992
Other (OTH)
AF:
AC:
1204
AN:
2110
Allele Balance Distribution
Red line indicates average allele balance
Average allele balance: 0.500
Heterozygous variant carriers
0
1737
3473
5210
6946
8683
0.00
0.20
0.40
0.60
0.80
0.95
Allele balance
Age Distribution
Genome Het
Genome Hom
Variant carriers
0
740
1480
2220
2960
3700
<30
30-35
35-40
40-45
45-50
50-55
55-60
60-65
65-70
70-75
75-80
>80
Age
Alfa
AF:
Hom.:
Bravo
AF:
ClinVar
Not reported inComputational scores
Source:
Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
DANN
Benign
PhyloP100
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
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