rs842288

Variant names:

• chr3-16274808-C-G
• rs842288
• NM_138381.5:c.183+3086C>G

Your query was ambiguous. Multiple possible variants found:

• chr3-16274808-C-G
• chr3-16274808-C-T

Variant summary

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

The NM_001330670.3(OXNAD1):​c.237+3086C>G variant causes a intron 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)
• Consequence: OXNAD1 NM_001330670.3 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.237
• Publications: 7 publications found

Genes affected

OXNAD1 (HGNC:25128): (oxidoreductase NAD binding domain containing 1) Predicted to enable oxidoreductase activity. [provided by Alliance of Genome Resources, Apr 2022]

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=-0.94).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001330670.3. 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
	OXNAD1	NM_138381.5	MANE Select	c.183+3086C>G		intron	N/A	NP_612390.1
	OXNAD1	NM_001330670.3		c.237+3086C>G		intron	N/A	NP_001317599.1
	OXNAD1	NM_001330671.3		c.237+3086C>G		intron	N/A	NP_001317600.1

Ensembl Transcripts

Selected	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OXNAD1	ENST00000285083.10	TSL:1 MANE Select	c.183+3086C>G		intron	N/A	ENSP00000285083.5
	OXNAD1	ENST00000605932.5	TSL:1	c.183+3086C>G		intron	N/A	ENSP00000475547.1
	OXNAD1	ENST00000452581.5	TSL:1	n.119+3737C>G		intron	N/A	ENSP00000397374.1

Frequencies

GnomAD3 genomes Cov.: 32

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.94
CADD	Benign	1.0
DANN	Benign	0.34
PhyloP100		-0.24

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.0		Details are displayed if max score is > 0.2

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

Other links and lift over

dbSNP: rs842288; hg19: chr3-16316315;