rs2505568

Variant names:

• chr10-36522408-T-A
• rs2505568
• ENST00000440465.1:n.1827A>T

Your query was ambiguous. Multiple possible variants found:

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

Variant summary

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

Genes affected

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

ACMG classification

Our verdict: Likely_benign. The variant received -4 ACMG points.

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

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.1827A>T		non_coding_transcript_exon	Exon 1 of 1

Frequencies

GnomAD3 genomes AF: 0.562 AC: 84730 AN: 150696 Hom.: 24008 Cov.: 26

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

African (AFR) AF: 0.483 AC: 58 AN: 120

American (AMR) AF: 0.530 AC: 367 AN: 692

Ashkenazi Jewish (ASJ) AF: 0.567 AC: 59 AN: 104

East Asian (EAS) AF: 0.587 AC: 101 AN: 172

South Asian (SAS) AF: 0.587 AC: 203 AN: 346

European-Finnish (FIN) AF: 0.687 AC: 327 AN: 476

Middle Eastern (MID) AF: 0.500 AC: 5 AN: 10

European-Non Finnish (NFE) AF: 0.571 AC: 2383 AN: 4176

Other (OTH) AF: 0.595 AC: 175 AN: 294

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

African (AFR) AF: 0.508 AC: 20843 AN: 41036

American (AMR) AF: 0.552 AC: 8338 AN: 15110

Ashkenazi Jewish (ASJ) AF: 0.578 AC: 1998 AN: 3454

East Asian (EAS) AF: 0.582 AC: 2961 AN: 5084

South Asian (SAS) AF: 0.593 AC: 2815 AN: 4750

European-Finnish (FIN) AF: 0.647 AC: 6744 AN: 10424

Middle Eastern (MID) AF: 0.582 AC: 171 AN: 294

European-Non Finnish (NFE) AF: 0.581 AC: 39295 AN: 67676

Other (OTH) AF: 0.539 AC: 1119 AN: 2076

Alfa AF: 0.582 Hom.: 2777

Bravo AF: 0.551

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.61
CADD	Benign	14
DANN	Benign	0.61
PhyloP100		3.2

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: rs2505568;

hg19: chr10-36811336;