Variant 11-71472431-C-T details in Genebe, Genetics Data Aggregator

Variant summary

Our verdict is Benign. Variant got -20 ACMG points: 0P and 20B. BP4_StrongBP6_Very_StrongBA1

The NM_018161.5(NADSYN1):c.408-18C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.68 in 1,591,738 control chromosomes in the GnomAD database, including 392,726 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.56 ( 26481 hom., cov: 33)

Exomes 𝑓: 0.69 ( 366245 hom. )

Consequence

NADSYN1
NM_018161.5 intron

Scores

Clinical Significance

Benign criteria provided, multiple submitters, no conflicts B:2

Conservation

PhyloP100: -1.99

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]

NADSYN1 links:

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ACMG classification

Classification made for transcript

Verdict is Benign. Variant got -20 ACMG points.

BP4

Computational evidence support a benign effect (BayesDel_noAF=-0.93).

BP6

Variant 11-71472431-C-T is Benign according to our data. Variant chr11-71472431-C-T is described in ClinVar as [Benign]. Clinvar id is 1321839.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.738 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt
NADSYN1	NM_018161.5 linkuse as main transcript	c.408-18C>T		intron_variant		ENST00000319023.7

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt
NADSYN1	ENST00000319023.7 linkuse as main transcript	c.408-18C>T		intron_variant		1	NM_018161.5	P1	Q6IA69-1

Frequencies

GnomAD3 genomes

AF:

0.558

AC:

84652

AN:

151586

Hom.:

26475

Cov.:

show subpopulations

Gnomad AFR

AF:

0.322

Gnomad AMI

AF:

0.688

Gnomad AMR

AF:

0.493

Gnomad ASJ

AF:

0.618

Gnomad EAS

AF:

0.440

Gnomad SAS

AF:

0.213

Gnomad FIN

AF:

0.585

Gnomad MID

AF:

0.443

Gnomad NFE

AF:

0.743

Gnomad OTH

AF:

0.537

GnomAD3 exomes

AF:

0.564

AC:

141521

AN:

251076

Hom.:

44239

AF XY:

0.559

AC XY:

75880

AN XY:

135676

show subpopulations

Gnomad AFR exome

AF:

0.315

Gnomad AMR exome

AF:

0.481

Gnomad ASJ exome

AF:

0.623

Gnomad EAS exome

AF:

0.448

Gnomad SAS exome

AF:

0.215

Gnomad FIN exome

AF:

0.598

Gnomad NFE exome

AF:

0.723

Gnomad OTH exome

AF:

0.606

GnomAD4 exome

AF:

0.692

AC:

997218

AN:

1440034

Hom.:

366245

Cov.:

AF XY:

0.679

AC XY:

487195

AN XY:

717558

show subpopulations

Gnomad4 AFR exome

AF:

0.301

Gnomad4 AMR exome

AF:

0.482

Gnomad4 ASJ exome

AF:

0.624

Gnomad4 EAS exome

AF:

0.410

Gnomad4 SAS exome

AF:

0.221

Gnomad4 FIN exome

AF:

0.606

Gnomad4 NFE exome

AF:

0.770

Gnomad4 OTH exome

AF:

0.638

GnomAD4 genome

AF:

0.558

AC:

84677

AN:

151704

Hom.:

26481

Cov.:

AF XY:

0.542

AC XY:

40147

AN XY:

74114

show subpopulations

Gnomad4 AFR

AF:

0.322

Gnomad4 AMR

AF:

0.493

Gnomad4 ASJ

AF:

0.618

Gnomad4 EAS

AF:

0.440

Gnomad4 SAS

AF:

0.214

Gnomad4 FIN

AF:

0.585

Gnomad4 NFE

AF:

0.743

Gnomad4 OTH

AF:

0.532

Alfa

AF:

0.594

Hom.:

3806

Bravo

AF:

0.552

Asia WGS

AF:

0.313

AC:

1092

AN:

3478

ClinVar

Significance: Benign

Submissions summary: Benign:2

Revision: criteria provided, multiple submitters, no conflicts

LINK: link

Submissions by phenotype

Vertebral, cardiac, renal, and limb defects syndrome 3

Benign:1

Benign, criteria provided, single submitter

clinical testing

Genome-Nilou Lab

Sep 05, 2021

- -

not provided

Benign:1

Benign, criteria provided, single submitter

not provided

Breakthrough Genomics, Breakthrough Genomics

- -

Computational scores

Source: dbNSFP v4.3

Name

Calibrated prediction

Score

Prediction

BayesDel_noAF

Benign

-0.93

CADD

Benign

0.010

DANN

Benign

0.41

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

Below is the list of publications found by LitVar. It may be empty.

Variant summary

Frequency

Consequence

Scores

Clinical Significance

Conservation

ACMG classification

Transcripts

RefSeq

Ensembl

Frequencies

ClinVar

Submissions by phenotype

Computational scores

Splicing

Publications

LitVar

Other links and lift over