11-71510528-T-C

Position:

• chr11-71510528-T-C

Variant summary

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

The variant allele was found at a frequency of 0.656 in 152,158 control chromosomes in the GnomAD database, including 34,291 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 0.66 (34291 hom., cov: 32)
• Consequence: S100A11P3 intragenic
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.667

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]

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.99).
• BA1: GnomAd4 highest subpopulation (NFE) allele frequency at 95% confidence interval = 0.788 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt
S100A11P3		n.71510528T>C		intragenic_variant

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NADSYN1	ENST00000527963.1	n.*74+9102T>C		intron_variant		4		ENSP00000435570.1

Frequencies

GnomAD3 genomes AF: 0.656 AC: 99789 AN: 152040 Hom.: 34275 Cov.: 32

Gnomad AFR AF: 0.518

Gnomad AMI AF: 0.716

Gnomad AMR AF: 0.556

Gnomad ASJ AF: 0.693

Gnomad EAS AF: 0.525

Gnomad SAS AF: 0.332

Gnomad FIN AF: 0.663

Gnomad MID AF: 0.544

Gnomad NFE AF: 0.793

Gnomad OTH AF: 0.635

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

GnomAD4 genome AF: 0.656 AC: 99821 AN: 152158 Hom.: 34291 Cov.: 32 AF XY: 0.642 AC XY: 47713 AN XY: 74376

Gnomad4 AFR AF: 0.517

Gnomad4 AMR AF: 0.556

Gnomad4 ASJ AF: 0.693

Gnomad4 EAS AF: 0.525

Gnomad4 SAS AF: 0.334

Gnomad4 FIN AF: 0.663

Gnomad4 NFE AF: 0.793

Gnomad4 OTH AF: 0.629

Alfa AF: 0.752 Hom.: 86595

Bravo AF: 0.647

Asia WGS AF: 0.391 AC: 1360 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.99
CADD	Benign	4.4
DANN	Benign	0.63

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs7940244; hg19: chr11-71221574;