rs2503084

Variant names:

• chr10-36523434-C-T
• rs2503084
• ENST00000440465.1:n.801G>A

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 8 publications found

Genes affected

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

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000440465.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMPTP1	ENST00000440465.1	TSL:6	n.801G>A		non_coding_transcript_exon	Exon 1 of 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

GnomAD2 exomes AF: 0.546 AC: 135461 AN: 248240 AF XY: 0.553

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 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

African (AFR) AF: 0.304 AC: 10106 AN: 33200

American (AMR) AF: 0.519 AC: 23039 AN: 44362

Ashkenazi Jewish (ASJ) AF: 0.559 AC: 14433 AN: 25828

East Asian (EAS) AF: 0.559 AC: 21986 AN: 39314

South Asian (SAS) AF: 0.591 AC: 50123 AN: 84876

European-Finnish (FIN) AF: 0.655 AC: 34870 AN: 53214

Middle Eastern (MID) AF: 0.557 AC: 3156 AN: 5668

European-Non Finnish (NFE) AF: 0.550 AC: 589941 AN: 1071768

Other (OTH) AF: 0.545 AC: 32089 AN: 58870

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

African (AFR) AF: 0.320 AC: 13216 AN: 41348

American (AMR) AF: 0.529 AC: 8067 AN: 15260

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 2005 AN: 3470

East Asian (EAS) AF: 0.581 AC: 2998 AN: 5156

South Asian (SAS) AF: 0.591 AC: 2844 AN: 4812

European-Finnish (FIN) AF: 0.648 AC: 6825 AN: 10536

Middle Eastern (MID) AF: 0.541 AC: 159 AN: 294

European-Non Finnish (NFE) AF: 0.579 AC: 39341 AN: 67954

Other (OTH) AF: 0.492 AC: 1037 AN: 2108

Alfa AF: 0.551 Hom.: 7537

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.47
CADD	Benign	3.5
DANN	Benign	0.40
PhyloP100		1.2
Mutation Taster		=100/0	polymorphism (auto)

Splicing

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs2503084;

hg19: chr10-36812362;