Variant chr11-71463507-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.317+22C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.231 in 1,608,888 control chromosomes in the GnomAD database, including 49,434 homozygotes. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Benign (★★).

Frequency

Genomes: 𝑓 0.28 ( 6522 hom., cov: 33)

Exomes 𝑓: 0.23 ( 42912 hom. )

Consequence

NADSYN1
NM_018161.5 intron

Scores

Clinical Significance

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

Conservation

PhyloP100: -2.14

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=-0.92).

BP6

Variant 11-71463507-C-T is Benign according to our data. Variant chr11-71463507-C-T is described in ClinVar as [Benign]. Clinvar id is 1321837.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars.

BA1

GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.441 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
NADSYN1	NM_018161.5 linkuse as main transcript	c.317+22C>T		intron_variant		ENST00000319023.7	NP_060631.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NADSYN1	ENST00000319023.7 linkuse as main transcript	c.317+22C>T		intron_variant		1	NM_018161.5	ENSP00000326424	P1	Q6IA69-1

Frequencies

GnomAD3 genomes

AF:

0.281

AC:

42765

AN:

151934

Hom.:

6525

Cov.:

show subpopulations

Gnomad AFR

AF:

0.339

Gnomad AMI

AF:

0.313

Gnomad AMR

AF:

0.301

Gnomad ASJ

AF:

0.219

Gnomad EAS

AF:

0.397

Gnomad SAS

AF:

0.459

Gnomad FIN

AF:

0.356

Gnomad MID

AF:

0.377

Gnomad NFE

AF:

0.211

Gnomad OTH

AF:

0.316

GnomAD3 exomes

AF:

0.286

AC:

70566

AN:

247108

Hom.:

10996

AF XY:

0.292

AC XY:

39129

AN XY:

133864

show subpopulations

Gnomad AFR exome

AF:

0.343

Gnomad AMR exome

AF:

0.226

Gnomad ASJ exome

AF:

0.227

Gnomad EAS exome

AF:

0.399

Gnomad SAS exome

AF:

0.459

Gnomad FIN exome

AF:

0.347

Gnomad NFE exome

AF:

0.224

Gnomad OTH exome

AF:

0.271

GnomAD4 exome

AF:

0.225

AC:

328304

AN:

1456836

Hom.:

42912

Cov.:

AF XY:

0.233

AC XY:

169108

AN XY:

724868

show subpopulations

Gnomad4 AFR exome

AF:

0.353

Gnomad4 AMR exome

AF:

0.233

Gnomad4 ASJ exome

AF:

0.224

Gnomad4 EAS exome

AF:

0.457

Gnomad4 SAS exome

AF:

0.461

Gnomad4 FIN exome

AF:

0.338

Gnomad4 NFE exome

AF:

0.188

Gnomad4 OTH exome

AF:

0.248

GnomAD4 genome

AF:

0.281

AC:

42758

AN:

152052

Hom.:

6522

Cov.:

AF XY:

0.294

AC XY:

21808

AN XY:

74302

show subpopulations

Gnomad4 AFR

AF:

0.338

Gnomad4 AMR

AF:

0.300

Gnomad4 ASJ

AF:

0.219

Gnomad4 EAS

AF:

0.397

Gnomad4 SAS

AF:

0.457

Gnomad4 FIN

AF:

0.356

Gnomad4 NFE

AF:

0.210

Gnomad4 OTH

AF:

0.319

Alfa

AF:

0.242

Hom.:

1015

Bravo

AF:

0.271

Asia WGS

AF:

0.371

AC:

1288

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

-0.92

CADD

Benign

0.048

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

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