16-16232681-G-A

Variant names:

• chr16-16232681-G-A
• rs936063009
• NM_001004067.4:c.15G>A

Variant summary

Our verdict is Likely benign. The variant received -5 ACMG points: 0P and 5B. BP4_Strong BP7

The NM_001004067.4(NOMO3):​c.15G>A​(p.Gln5Gln) variant causes a synonymous change involving the alteration of a non-conserved nucleotide. 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 0.0000074 (0 hom., cov: 19)
• Consequence: NOMO3 NM_001004067.4 synonymous
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 1.72
• Publications: 0 publications found

Genes affected

NOMO3 (HGNC:25242): (NODAL modulator 3) This gene encodes a protein originally thought to be related to the collagenase gene family. This gene is one of three highly similar genes in a duplicated region on the short arm of chromosome 16. These three genes encode closely related proteins that may have the same function. The protein encoded by one of these genes has been identified as part of a protein complex that participates in the Nodal signaling pathway during vertebrate development. Mutations in ABCC6, which is located nearby, rather than mutations in this gene are associated with pseudoxanthoma elasticum. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Likely_benign. The variant received -5 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.93).
• BP7: Synonymous conserved (PhyloP=1.72 with no splicing effect.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001004067.4. 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
	NOMO3	NM_001004067.4	MANE Select	c.15G>A	p.Gln5Gln	synonymous	Exon 1 of 31	NP_001004067.1	P69849

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NOMO3	ENST00000399336.9	TSL:1 MANE Select	c.15G>A	p.Gln5Gln	synonymous	Exon 1 of 31	ENSP00000382274.4	P69849
	NOMO3	ENST00000263012.10	TSL:1	c.15G>A	p.Gln5Gln	synonymous	Exon 1 of 32	ENSP00000263012.6	J3KN36
	NOMO3	ENST00000575225.5	TSL:1	n.15G>A		non_coding_transcript_exon	Exon 1 of 31	ENSP00000458267.1	I3L0Q6

Frequencies

GnomAD3 genomes AF: 0.00000738 AC: 1 AN: 135566 Hom.: 0 Cov.: 19

Gnomad AFR AF: 0.00

Gnomad AMI AF: 0.00

Gnomad AMR AF: 0.00

Gnomad ASJ AF: 0.00

Gnomad EAS AF: 0.00

Gnomad SAS AF: 0.00

Gnomad FIN AF: 0.00

Gnomad MID AF: 0.00

Gnomad NFE AF: 0.0000158

Gnomad OTH AF: 0.00

GnomAD4 exome Cov.: 10

GnomAD4 genome AF: 0.00000738 AC: 1 AN: 135566 Hom.: 0 Cov.: 19 AF XY: 0.0000153 AC XY: 1 AN XY: 65316

African (AFR) AF: 0.00 AC: 0 AN: 35078

American (AMR) AF: 0.00 AC: 0 AN: 13674

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 3266

East Asian (EAS) AF: 0.00 AC: 0 AN: 4364

South Asian (SAS) AF: 0.00 AC: 0 AN: 3862

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 9122

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 290

European-Non Finnish (NFE) AF: 0.0000158 AC: 1 AN: 63330

Other (OTH) AF: 0.00 AC: 0 AN: 1768

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.93
CADD	Benign	8.8
DANN	Benign	0.93
PhyloP100		1.7
PromoterAI		0.015	Neutral

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: rs936063009; hg19: chr16-16326538;