rs2505568

Positions:

• chr10-36522408-T-A
• chr10-36522408-T-G

Variant summary

Our verdict is Likely benign. Variant got -4 ACMG points: 0P and 4B. BP4_Strong

The ENST00000440465.1(NAMPTP1):​n.1827A>T variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. 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 0.56 (24011 hom., cov: 26)
  • Exomes 𝑓: 0.58 (1084 hom.)
  • Failed GnomAD Quality Control
• Consequence: NAMPTP1 ENST00000440465.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.22

Genes affected

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

ACMG classification

Verdict is Likely_benign. Variant got -4 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.61).

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.1827A>T		non_coding_transcript_exon_variant	1/1

Frequencies

GnomAD3 genomes AF: 0.00 AC: 84730 AN: 150696 Hom.: 24008 Cov.: 26 FAILED QC

Gnomad AFR AF: 0.508

Gnomad AMI AF: 0.533

Gnomad AMR AF: 0.552

Gnomad ASJ AF: 0.578

Gnomad EAS AF: 0.582

Gnomad SAS AF: 0.593

Gnomad FIN AF: 0.647

Gnomad MID AF: 0.595

Gnomad NFE AF: 0.581

Gnomad OTH AF: 0.541

GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.576 AC: 3678 AN: 6390 Hom.: 1084 Cov.: 0 AF XY: 0.586 AC XY: 1947 AN XY: 3324

Gnomad4 AFR exome AF: 0.483

Gnomad4 AMR exome AF: 0.530

Gnomad4 ASJ exome AF: 0.567

Gnomad4 EAS exome AF: 0.587

Gnomad4 SAS exome AF: 0.587

Gnomad4 FIN exome AF: 0.687

Gnomad4 NFE exome AF: 0.571

Gnomad4 OTH exome AF: 0.595

GnomAD4 genome Data not reliable, filtered out with message: AS_VQSR AF: 0.562 AC: 84769 AN: 150814 Hom.: 24011 Cov.: 26 AF XY: 0.566 AC XY: 41664 AN XY: 73644

Gnomad4 AFR AF: 0.508

Gnomad4 AMR AF: 0.552

Gnomad4 ASJ AF: 0.578

Gnomad4 EAS AF: 0.582

Gnomad4 SAS AF: 0.593

Gnomad4 FIN AF: 0.647

Gnomad4 NFE AF: 0.581

Gnomad4 OTH AF: 0.539

Alfa AF: 0.582 Hom.: 2777

Bravo AF: 0.551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.61

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs2505568; hg19: chr10-36811336;