rs11234027

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_StrongBA1

The ENST00000527963.1(NADSYN1):​n.*190-935G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.236 in 152,126 control chromosomes in the GnomAD database, including 4,734 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 0.24 ( 4734 hom., cov: 33)

Consequence

NADSYN1
ENST00000527963.1 intron

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: -0.328
Variant links:
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]

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -12 ACMG points.

BP4
Computational evidence support a benign effect (BayesDel_noAF=-0.7).
BA1
GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.322 is higher than 0.05.

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect Exon rank MANE Protein UniProt

Ensembl

Gene Transcript HGVSc HGVSp Effect Exon rank TSL MANE Protein Appris UniProt
NADSYN1ENST00000527963.1 linkn.*190-935G>A intron_variant Intron 3 of 3 4 ENSP00000435570.1 H0YED2

Frequencies

GnomAD3 genomes
AF:
0.236
AC:
35822
AN:
152008
Hom.:
4711
Cov.:
33
show subpopulations
Gnomad AFR
AF:
0.320
Gnomad AMI
AF:
0.282
Gnomad AMR
AF:
0.262
Gnomad ASJ
AF:
0.144
Gnomad EAS
AF:
0.318
Gnomad SAS
AF:
0.338
Gnomad FIN
AF:
0.282
Gnomad MID
AF:
0.285
Gnomad NFE
AF:
0.161
Gnomad OTH
AF:
0.258
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome
AF:
0.236
AC:
35876
AN:
152126
Hom.:
4734
Cov.:
33
AF XY:
0.246
AC XY:
18301
AN XY:
74360
show subpopulations
Gnomad4 AFR
AF:
0.321
Gnomad4 AMR
AF:
0.261
Gnomad4 ASJ
AF:
0.144
Gnomad4 EAS
AF:
0.318
Gnomad4 SAS
AF:
0.335
Gnomad4 FIN
AF:
0.282
Gnomad4 NFE
AF:
0.161
Gnomad4 OTH
AF:
0.261
Alfa
AF:
0.187
Hom.:
1880
Bravo
AF:
0.234
Asia WGS
AF:
0.311
AC:
1080
AN:
3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.70
CADD
Benign
0.25
DANN
Benign
0.70

Splicing

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: rs11234027; hg19: chr11-71234107; API