rs10898191

Positions:

• chr11-71483555-G-A
• chr11-71483555-G-T

Variant summary

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

The ENST00000319023.7(NADSYN1):​c.1319+538G>A variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.235 in 152,056 control chromosomes in the GnomAD database, including 4,701 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 (4701 hom., cov: 33)
• Consequence: NADSYN1 ENST00000319023.7 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.09

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=-0.97).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.343 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NADSYN1	NM_018161.5	c.1319+538G>A		intron_variant		ENST00000319023.7	NP_060631.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NADSYN1	ENST00000319023.7	c.1319+538G>A		intron_variant		1	NM_018161.5	ENSP00000326424	P1

Frequencies

GnomAD3 genomes AF: 0.235 AC: 35747 AN: 151938 Hom.: 4685 Cov.: 33

Gnomad AFR AF: 0.318

Gnomad AMI AF: 0.264

Gnomad AMR AF: 0.257

Gnomad ASJ AF: 0.140

Gnomad EAS AF: 0.315

Gnomad SAS AF: 0.359

Gnomad FIN AF: 0.283

Gnomad MID AF: 0.293

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: 0.235 AC: 35798 AN: 152056 Hom.: 4701 Cov.: 33 AF XY: 0.246 AC XY: 18279 AN XY: 74332

Gnomad4 AFR AF: 0.319

Gnomad4 AMR AF: 0.257

Gnomad4 ASJ AF: 0.140

Gnomad4 EAS AF: 0.315

Gnomad4 SAS AF: 0.357

Gnomad4 FIN AF: 0.283

Gnomad4 NFE AF: 0.161

Gnomad4 OTH AF: 0.262

Alfa AF: 0.115 Hom.: 203

Bravo AF: 0.233

Asia WGS AF: 0.318 AC: 1103 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.97
CADD	Benign	0.20
DANN	Benign	0.56

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: rs10898191; hg19: chr11-71194601;