rs2503084

Positions:

• chr10-36523434-C-T

Variant summary

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

The ENST00000440465.1(NAMPTP1):​n.801G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.546 in 1,568,948 control chromosomes in the GnomAD database, including 225,981 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 0.51 (20758 hom., cov: 31)
  • Exomes 𝑓: 0.55 (205223 hom.)
• Consequence: NAMPTP1 ENST00000440465.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.18

Genes affected

NAMPTP1 (HGNC:17633): (nicotinamide phosphoribosyltransferase pseudogene 1)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.47).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.574 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NAMPTP1	ENST00000440465.1	n.801G>A		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.507 AC: 76988 AN: 151730 Hom.: 20771 Cov.: 31

Gnomad AFR AF: 0.320

Gnomad AMI AF: 0.532

Gnomad AMR AF: 0.529

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.581

Gnomad SAS AF: 0.592

Gnomad FIN AF: 0.648

Gnomad MID AF: 0.554

Gnomad NFE AF: 0.579

Gnomad OTH AF: 0.493

GnomAD3 exomes AF: 0.546 AC: 135461 AN: 248240 Hom.: 35868 AF XY: 0.553 AC XY: 74076 AN XY: 134062

Gnomad AFR exome AF: 0.310

Gnomad AMR exome AF: 0.506

Gnomad ASJ exome AF: 0.548

Gnomad EAS exome AF: 0.552

Gnomad SAS exome AF: 0.583

Gnomad FIN exome AF: 0.640

Gnomad NFE exome AF: 0.562

Gnomad OTH exome AF: 0.551

GnomAD4 exome AF: 0.550 AC: 779743 AN: 1417100 Hom.: 205223 Cov.: 44 AF XY: 0.553 AC XY: 391081 AN XY: 706652

Gnomad4 AFR exome AF: 0.304

Gnomad4 AMR exome AF: 0.519

Gnomad4 ASJ exome AF: 0.559

Gnomad4 EAS exome AF: 0.559

Gnomad4 SAS exome AF: 0.591

Gnomad4 FIN exome AF: 0.655

Gnomad4 NFE exome AF: 0.550

Gnomad4 OTH exome AF: 0.545

GnomAD4 genome AF: 0.507 AC: 76976 AN: 151848 Hom.: 20758 Cov.: 31 AF XY: 0.513 AC XY: 38099 AN XY: 74196

Gnomad4 AFR AF: 0.320

Gnomad4 AMR AF: 0.529

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.581

Gnomad4 SAS AF: 0.591

Gnomad4 FIN AF: 0.648

Gnomad4 NFE AF: 0.579

Gnomad4 OTH AF: 0.492

Alfa AF: 0.555 Hom.: 7499

Bravo AF: 0.486

Asia WGS AF: 0.552 AC: 1919 AN: 3478

EpiCase AF: 0.569

EpiControl AF: 0.554

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	3.5
DANN	Benign	0.40

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2503084; hg19: chr10-36812362;