chr7-106286419-G-A

Variant names:

• chr7-106286419-G-A
• rs61330082
• ENST00000609281.3:n.*93G>A

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000609281.3(NAMPT-AS1):​n.*93G>A variant causes a downstream gene change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.23 in 152,176 control chromosomes in the GnomAD database, including 4,697 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 0.23 (4695 hom., cov: 33)
  • Exomes 𝑓: 0.40 (2 hom.)
• Consequence: NAMPT-AS1 ENST00000609281.3 downstream_gene
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.191
• Publications: 49 publications found

Genes affected

NAMPT-AS1 (HGNC:56696): (NAMPT antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.82).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.471 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000609281.3. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMPT-AS1	NR_186647.1		n.*93G>A		downstream_gene	N/A

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NAMPT-AS1	ENST00000609281.3	TSL:6	n.*93G>A		downstream_gene	N/A

Frequencies

GnomAD3 genomes AF: 0.230 AC: 34978 AN: 152036 Hom.: 4689 Cov.: 33

Gnomad AFR AF: 0.107

Gnomad AMI AF: 0.208

Gnomad AMR AF: 0.324

Gnomad ASJ AF: 0.262

Gnomad EAS AF: 0.486

Gnomad SAS AF: 0.254

Gnomad FIN AF: 0.305

Gnomad MID AF: 0.225

Gnomad NFE AF: 0.249

Gnomad OTH AF: 0.247

GnomAD4 exome AF: 0.400 AC: 8 AN: 20 Hom.: 2 AF XY: 0.313 AC XY: 5 AN XY: 16

African (AFR) AC: 0 AN: 0

American (AMR) AC: 0 AN: 0

Ashkenazi Jewish (ASJ) AC: 0 AN: 0

East Asian (EAS) AC: 0 AN: 0

South Asian (SAS) AF: 0.500 AC: 1 AN: 2

European-Finnish (FIN) AF: 0.250 AC: 1 AN: 4

Middle Eastern (MID) AC: 0 AN: 0

European-Non Finnish (NFE) AF: 0.500 AC: 6 AN: 12

Other (OTH) AF: 0.00 AC: 0 AN: 2

GnomAD4 genome AF: 0.230 AC: 35005 AN: 152156 Hom.: 4695 Cov.: 33 AF XY: 0.236 AC XY: 17574 AN XY: 74372

African (AFR) AF: 0.107 AC: 4451 AN: 41542

American (AMR) AF: 0.323 AC: 4944 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.262 AC: 908 AN: 3470

East Asian (EAS) AF: 0.487 AC: 2521 AN: 5180

South Asian (SAS) AF: 0.256 AC: 1235 AN: 4830

European-Finnish (FIN) AF: 0.305 AC: 3216 AN: 10550

Middle Eastern (MID) AF: 0.224 AC: 66 AN: 294

European-Non Finnish (NFE) AF: 0.249 AC: 16942 AN: 67976

Other (OTH) AF: 0.252 AC: 532 AN: 2112

Alfa AF: 0.241 Hom.: 6354

Bravo AF: 0.229

Asia WGS AF: 0.372 AC: 1291 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.82
CADD	Benign	1.4
DANN	Benign	0.60
PhyloP100		-0.19
PromoterAI		-0.015	Neutral

Splicing

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

Other links and lift over

dbSNP: rs61330082; hg19: chr7-105926865;