rs9290923

Variant names:

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

Your query was ambiguous. Multiple possible variants found:

• chr3-190167465-G-A
• chr3-190167465-G-C

Variant summary

Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2 BP4_Strong

The ENST00000457517.1(NMNAT1P3):​n.702G>A variant causes a non coding transcript exon change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. 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: not found (cov: 32)
  • Exomes 𝑓: 0.0 (0 hom.)
  • Failed GnomAD Quality Control
• 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: Likely_benign. The variant received -2 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.59).

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>A		non_coding_transcript_exon	Exon 1 of 1
	P3H2-AS1	ENST00000747181.1		n.250+38390G>A		intron	N/A
	P3H2-AS1	ENST00000747182.1		n.286+38390G>A		intron	N/A

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Data not reliable, filtered out with message: AC0 AF: 0.00 AC: 0 AN: 9938 Hom.: 0 Cov.: 0 AF XY: 0.00 AC XY: 0 AN XY: 5328

African (AFR) AF: 0.00 AC: 0 AN: 110

American (AMR) AF: 0.00 AC: 0 AN: 402

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 72

East Asian (EAS) AF: 0.00 AC: 0 AN: 258

South Asian (SAS) AF: 0.00 AC: 0 AN: 260

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 5458

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 78

European-Non Finnish (NFE) AF: 0.00 AC: 0 AN: 2980

Other (OTH) AF: 0.00 AC: 0 AN: 320

GnomAD4 genome Cov.: 32

Alfa AF: 0.00 Hom.: 906

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.59
CADD	Benign	7.5
DANN	Benign	0.66
PhyloP100		0.84

Splicing

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

Other links and lift over

dbSNP: rs9290923; hg19: chr3-189885254;