rs375086415

Variant names:

• chr16-1979474-C-A
• rs375086415
• NM_172167.3:c.769G>T

Your query was ambiguous. Multiple possible variants found:

• chr16-1979474-C-A
• chr16-1979474-C-G
• chr16-1979474-C-T

Variant summary

Our verdict is Uncertain significance. Variant got 1 ACMG points: 2P and 1B. PM2 BP4

The NM_172167.3(NOXO1):​c.769G>T​(p.Ala257Ser) variant causes a missense 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. 12/21 in silico tools predict 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: 34)
• Consequence: NOXO1 NM_172167.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 3.01

Genes affected

NOXO1 (HGNC:19404): (NADPH oxidase organizer 1) This gene encodes an NADPH oxidase (NOX) organizer, which positively regulates NOX1 and NOX3. The protein contains a PX domain and two SH3 domains. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jun 2012]

TBL3 (HGNC:11587): (transducin beta like 3) The protein encoded by this gene has sequence similarity with members of the WD40 repeat-containing protein family. The WD40 group is a large family of proteins, which appear to have a regulatory function. It is believed that the WD40 repeats mediate protein-protein interactions and members of the family are involved in signal transduction, RNA processing, gene regulation, vesicular trafficking, cytoskeletal assembly and may play a role in the control of cytotypic differentiation. This gene has multiple polyadenylation sites. It might have multiple alternatively spliced transcript variants but the variants have not been fully described yet. [provided by RefSeq, Jul 2008]

ACMG classification

Verdict is Uncertain_significance. Variant got 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.30054176).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOXO1	NM_172167.3	c.769G>T	p.Ala257Ser	missense_variant	Exon 7 of 8	ENST00000356120.9	NP_751907.1
TBL3	NM_006453.3	c.*789C>A		3_prime_UTR_variant	Exon 22 of 22	ENST00000568546.6	NP_006444.2

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOXO1	ENST00000356120.9	c.769G>T	p.Ala257Ser	missense_variant	Exon 7 of 8	1	NM_172167.3	ENSP00000348435.4
TBL3	ENST00000568546.6	c.*789C>A		3_prime_UTR_variant	Exon 22 of 22	1	NM_006453.3	ENSP00000454836.1

Frequencies

GnomAD3 genomes Cov.: 34

GnomAD4 exome Cov.: 34

GnomAD4 genome Cov.: 34

Bravo AF: 0.00000378

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.13
BayesDel_addAF	Benign	-0.098	T
BayesDel_noAF	Benign	-0.38
CADD	Benign	23
DANN	Uncertain	0.98
DEOGEN2	Benign	0.098	.;.;T;.
Eigen	Benign	0.096
Eigen_PC	Benign	0.067
FATHMM_MKL	Benign	0.68	D
LIST_S2	Benign	0.75	T;T;T;T
M_CAP	Uncertain	0.090	D
MetaRNN	Benign	0.30	T;T;T;T
MetaSVM	Benign	-0.63	T
MutationAssessor	Benign	1.8	.;.;L;.
PrimateAI	Uncertain	0.59	T
PROVEAN	Benign	-1.5	N;N;N;N
REVEL	Benign	0.15
Sift	Benign	0.23	T;T;T;T
Sift4G	Benign	0.54	T;T;T;T
Polyphen		0.81	P;P;P;P
Vest4		0.28
MutPred		0.56		.;.;Gain of phosphorylation at A262 (P = 0.0187);.;
MVP		0.62
MPC		0.86
ClinPred		0.81	D
GERP RS		5.1
Varity_R		0.17
gMVP		0.27

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

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

Publications

LitVar

Other links and lift over

dbSNP: rs375086415; hg19: chr16-2029475;