rs11234027

chr11-71523061-G-A

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000527963.1(NADSYN1):c.*190-935G>A variant causes a intron, NMD transcript 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, NMD_transcript
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.328

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]

ACMG classification

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/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NADSYN1	ENST00000527963.1	c.*190-935G>A		intron_variant, NMD_transcript_variant		4

Frequencies

GnomAD3 genomes AF: 0.236 AC: 35822 AN: 152008 Hom.: 4711 Cov.: 33

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

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

Other links and lift over

dbSNP: rs11234027; hg19: chr11-71234107;