rs10898201

Positions:

• chr11-71490481-C-A
• chr11-71490481-C-T

Variant summary

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

The NM_018161.5(NADSYN1):​c.1563-364C>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.201 in 152,052 control chromosomes in the GnomAD database, including 3,408 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 0.20 (3408 hom., cov: 33)
• Consequence: NADSYN1 NM_018161.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.303

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=-0.88).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.361 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NADSYN1	NM_018161.5	c.1563-364C>A		intron_variant		ENST00000319023.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NADSYN1	ENST00000319023.7	c.1563-364C>A		intron_variant		1	NM_018161.5	P1

Frequencies

GnomAD3 genomes AF: 0.201 AC: 30602 AN: 151934 Hom.: 3409 Cov.: 33

Gnomad AFR AF: 0.198

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.245

Gnomad ASJ AF: 0.137

Gnomad EAS AF: 0.376

Gnomad SAS AF: 0.342

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.269

Gnomad NFE AF: 0.159

Gnomad OTH AF: 0.228

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.201 AC: 30589 AN: 152052 Hom.: 3408 Cov.: 33 AF XY: 0.212 AC XY: 15752 AN XY: 74302

Gnomad4 AFR AF: 0.198

Gnomad4 AMR AF: 0.245

Gnomad4 ASJ AF: 0.137

Gnomad4 EAS AF: 0.375

Gnomad4 SAS AF: 0.340

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.159

Gnomad4 OTH AF: 0.233

Alfa AF: 0.183 Hom.: 332

Bravo AF: 0.194

Asia WGS AF: 0.336 AC: 1166 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.88
CADD	Benign	3.1
DANN	Benign	0.87

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

Other links and lift over

dbSNP: rs10898201; hg19: chr11-71201527;