3-190167465-G-C

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -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
• Publications: 2 publications found

Genes affected

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

P3H2-AS1 (HGNC:40886): (P3H2 antisense RNA 1)

ACMG classification

Our verdict: Benign. The variant received -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.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000457517.1. 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
	NMNAT1P3	ENST00000457517.1	TSL:6	n.702G>C		non_coding_transcript_exon	Exon 1 of 1
	P3H2-AS1	ENST00000747181.1		n.250+38390G>C		intron	N/A
	P3H2-AS1	ENST00000747182.1		n.286+38390G>C		intron	N/A

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

African (AFR) AF: 0.355 AC: 39 AN: 110

American (AMR) AF: 0.427 AC: 170 AN: 398

Ashkenazi Jewish (ASJ) AF: 0.306 AC: 22 AN: 72

East Asian (EAS) AF: 0.287 AC: 74 AN: 258

South Asian (SAS) AF: 0.565 AC: 147 AN: 260

European-Finnish (FIN) AF: 0.378 AC: 2052 AN: 5422

Middle Eastern (MID) AF: 0.449 AC: 35 AN: 78

European-Non Finnish (NFE) AF: 0.353 AC: 1047 AN: 2962

Other (OTH) AF: 0.349 AC: 111 AN: 318

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

African (AFR) AF: 0.308 AC: 12765 AN: 41488

American (AMR) AF: 0.307 AC: 4698 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.300 AC: 1042 AN: 3468

East Asian (EAS) AF: 0.255 AC: 1319 AN: 5170

South Asian (SAS) AF: 0.498 AC: 2393 AN: 4810

European-Finnish (FIN) AF: 0.366 AC: 3860 AN: 10548

Middle Eastern (MID) AF: 0.299 AC: 88 AN: 294

European-Non Finnish (NFE) AF: 0.314 AC: 21328 AN: 67972

Other (OTH) AF: 0.308 AC: 650 AN: 2110

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 v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.67
CADD	Benign	7.0
DANN	Benign	0.59
PhyloP100		0.84

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: rs9290923;

hg19: chr3-189885254;

COSMIC: COSV66920415;