rs4945008

Variant names:

• chr11-71510202-A-G
• rs4945008

Your query was ambiguous. Multiple possible variants found:

• chr11-71510202-A-G
• chr11-71510202-A-T

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.526 in 152,150 control chromosomes in the GnomAD database, including 25,135 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 0.53 (25135 hom., cov: 33)
• Consequence: S100A11P3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.164
• Publications: 27 publications found

Genes affected

S100A11P3 (HGNC:37842):

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 Gene-Disease associations (from GenCC):

• vertebral, cardiac, renal, and limb defects syndrome 3

  Inheritance: AR Classification: STRONG, MODERATE, LIMITED Submitted by: Ambry Genetics, G2P, Labcorp Genetics (formerly Invitae)
• congenital vertebral-cardiac-renal anomalies syndrome

  Inheritance: AR Classification: SUPPORTIVE Submitted by: Orphanet

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.96).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.734 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
S100A11P3		n.71510202A>G		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NADSYN1	ENST00000527963.1	n.*74+8776A>G		intron_variant	Intron 2 of 3	4		ENSP00000435570.1

Frequencies

GnomAD3 genomes AF: 0.526 AC: 80033 AN: 152030 Hom.: 25131 Cov.: 33

Gnomad AFR AF: 0.221

Gnomad AMI AF: 0.702

Gnomad AMR AF: 0.486

Gnomad ASJ AF: 0.610

Gnomad EAS AF: 0.381

Gnomad SAS AF: 0.208

Gnomad FIN AF: 0.588

Gnomad MID AF: 0.434

Gnomad NFE AF: 0.740

Gnomad OTH AF: 0.517

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

GnomAD4 genome AF: 0.526 AC: 80044 AN: 152150 Hom.: 25135 Cov.: 33 AF XY: 0.511 AC XY: 38013 AN XY: 74382

African (AFR) AF: 0.221 AC: 9152 AN: 41500

American (AMR) AF: 0.486 AC: 7427 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.610 AC: 2117 AN: 3472

East Asian (EAS) AF: 0.382 AC: 1976 AN: 5176

South Asian (SAS) AF: 0.210 AC: 1011 AN: 4820

European-Finnish (FIN) AF: 0.588 AC: 6222 AN: 10582

Middle Eastern (MID) AF: 0.452 AC: 133 AN: 294

European-Non Finnish (NFE) AF: 0.740 AC: 50287 AN: 67996

Other (OTH) AF: 0.511 AC: 1080 AN: 2112

Alfa AF: 0.548 Hom.: 3808

Bravo AF: 0.515

Asia WGS AF: 0.270 AC: 943 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.96
CADD	Benign	6.5
DANN	Benign	0.51
PhyloP100		0.16

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs4945008; hg19: chr11-71221248;