chr3-16274808-C-T

Variant names:

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

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_138381.5(OXNAD1):​c.183+3086C>T variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.679 in 152,126 control chromosomes in the GnomAD database, including 35,964 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 0.68 (35964 hom., cov: 32)
• Consequence: OXNAD1 NM_138381.5 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: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.02).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.829 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_138381.5. 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
	OXNAD1	NM_138381.5	MANE Select	c.183+3086C>T		intron	N/A	NP_612390.1	Q96HP4
	OXNAD1	NM_001330670.3		c.237+3086C>T		intron	N/A	NP_001317599.1	C9JLB7
	OXNAD1	NM_001330671.3		c.237+3086C>T		intron	N/A	NP_001317600.1	C9JLB7

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	OXNAD1	ENST00000285083.10	TSL:1 MANE Select	c.183+3086C>T		intron	N/A	ENSP00000285083.5	Q96HP4
	OXNAD1	ENST00000605932.5	TSL:1	c.183+3086C>T		intron	N/A	ENSP00000475547.1	Q96HP4
	OXNAD1	ENST00000452581.5	TSL:1	n.119+3737C>T		intron	N/A	ENSP00000397374.1	F8WB50

Frequencies

GnomAD3 genomes AF: 0.679 AC: 103159 AN: 152008 Hom.: 35926 Cov.: 32

Gnomad AFR AF: 0.836

Gnomad AMI AF: 0.677

Gnomad AMR AF: 0.669

Gnomad ASJ AF: 0.677

Gnomad EAS AF: 0.666

Gnomad SAS AF: 0.672

Gnomad FIN AF: 0.529

Gnomad MID AF: 0.718

Gnomad NFE AF: 0.610

Gnomad OTH AF: 0.686

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

GnomAD4 genome AF: 0.679 AC: 103257 AN: 152126 Hom.: 35964 Cov.: 32 AF XY: 0.676 AC XY: 50307 AN XY: 74366

African (AFR) AF: 0.836 AC: 34708 AN: 41514

American (AMR) AF: 0.669 AC: 10223 AN: 15288

Ashkenazi Jewish (ASJ) AF: 0.677 AC: 2349 AN: 3470

East Asian (EAS) AF: 0.666 AC: 3452 AN: 5186

South Asian (SAS) AF: 0.672 AC: 3240 AN: 4824

European-Finnish (FIN) AF: 0.529 AC: 5583 AN: 10562

Middle Eastern (MID) AF: 0.707 AC: 208 AN: 294

European-Non Finnish (NFE) AF: 0.610 AC: 41432 AN: 67972

Other (OTH) AF: 0.686 AC: 1447 AN: 2108

Alfa AF: 0.631 Hom.: 15728

Bravo AF: 0.694

Asia WGS AF: 0.694 AC: 2417 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	1.2
DANN	Benign	0.55
PhyloP100		-0.24
Mutation Taster		=100/0	polymorphism (auto)

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;