ENST00000457517.1:n.702G>C

Variant names:

• chr3-190167465-G-C
• rs9290923
• ENST00000457517.1:n.702G>C

Variant summary

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

The ENST00000457517.1(NMNAT1P3):​n.702G>C 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 0.322 in 161,926 control chromosomes in the GnomAD database, including 8,621 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 0.32 (7926 hom., cov: 32)
  • Exomes 𝑓: 0.37 (695 hom.)
• Consequence: NMNAT1P3 ENST00000457517.1 non_coding_transcript_exon
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.840

Genes affected

NMNAT1P3 (HGNC:49165): (NMNAT1 pseudogene 3)

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.67).
• BA1: GnomAd4 highest subpopulation (SAS) allele frequency at 95% confidence interval = 0.481 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NMNAT1P3	ENST00000457517.1	n.702G>C		non_coding_transcript_exon_variant	Exon 1 of 1	6

Frequencies

GnomAD3 genomes AF: 0.319 AC: 48421 AN: 151930 Hom.: 7914 Cov.: 32

Gnomad AFR AF: 0.307

Gnomad AMI AF: 0.366

Gnomad AMR AF: 0.308

Gnomad ASJ AF: 0.300

Gnomad EAS AF: 0.256

Gnomad SAS AF: 0.497

Gnomad FIN AF: 0.366

Gnomad MID AF: 0.297

Gnomad NFE AF: 0.314

Gnomad OTH AF: 0.303

GnomAD4 exome AF: 0.374 AC: 3697 AN: 9878 Hom.: 695 Cov.: 0 AF XY: 0.373 AC XY: 1978 AN XY: 5302

Gnomad4 AFR exome AF: 0.355

Gnomad4 AMR exome AF: 0.427

Gnomad4 ASJ exome AF: 0.306

Gnomad4 EAS exome AF: 0.287

Gnomad4 SAS exome AF: 0.565

Gnomad4 FIN exome AF: 0.378

Gnomad4 NFE exome AF: 0.353

Gnomad4 OTH exome AF: 0.349

GnomAD4 genome AF: 0.319 AC: 48475 AN: 152048 Hom.: 7926 Cov.: 32 AF XY: 0.321 AC XY: 23878 AN XY: 74318

Gnomad4 AFR AF: 0.308

Gnomad4 AMR AF: 0.307

Gnomad4 ASJ AF: 0.300

Gnomad4 EAS AF: 0.255

Gnomad4 SAS AF: 0.498

Gnomad4 FIN AF: 0.366

Gnomad4 NFE AF: 0.314

Gnomad4 OTH AF: 0.308

Alfa AF: 0.310 Hom.: 906

Bravo AF: 0.311

Asia WGS AF: 0.429 AC: 1489 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.0
DANN	Benign	0.59

Splicing

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

Publications

LitVar

Other links and lift over

dbSNP: rs9290923; hg19: chr3-189885254; COSMIC: COSV66920415;