3-190167465-G-C

Position:

• chr3-190167465-G-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:):

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/exons	MANE	Protein	UniProt
		n.190167465G>C		intergenic_region

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Protein	Appris	UniProt
NMNAT1P3	ENST00000457517.1	n.702G>C		non_coding_transcript_exon_variant	1/1	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;