7-144397490-G-C

Variant names:

• chr7-144397490-G-C
• NM_001080413.3:c.1826C>G

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2 BP4_Moderate

The NM_001080413.3(NOBOX):​c.1826C>G​(p.Pro609Arg) variant causes a missense change. 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: NOBOX NM_001080413.3 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 4.17

Genes affected

NOBOX (HGNC:22448): (NOBOX oogenesis homeobox) This homeobox gene encodes a transcription factor that is thought to play a role in oogenesis. In mice, it is essential for folliculogenesis and regulation of oocyte-specific genes. Defects in this gene result in premature ovarian failure type 5.[provided by RefSeq, May 2011]

ACMG classification

Verdict is Uncertain_significance. Variant got 0 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.23355862).

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
NOBOX	NM_001080413.3	c.1826C>G	p.Pro609Arg	missense_variant	Exon 10 of 10	ENST00000467773.1	NP_001073882.3
NOBOX	XM_017011742.3	c.1730C>G	p.Pro577Arg	missense_variant	Exon 10 of 10		XP_016867231.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
NOBOX	ENST00000467773.1	c.1826C>G	p.Pro609Arg	missense_variant	Exon 10 of 10	5	NM_001080413.3	ENSP00000419457.1
NOBOX	ENST00000483238.5	c.1730C>G	p.Pro577Arg	missense_variant	Exon 10 of 10	5		ENSP00000419565.1
NOBOX	ENST00000645489.1	c.1475C>G	p.Pro492Arg	missense_variant	Exon 8 of 8			ENSP00000496732.1
NOBOX	ENST00000643164.1	c.*21C>G		downstream_gene_variant				ENSP00000495343.1

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome Cov.: 31

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Benign	0.18
BayesDel_addAF	Uncertain	0.047	T
BayesDel_noAF	Benign	-0.17
CADD	Benign	21
DANN	Uncertain	1.0
DEOGEN2	Benign	0.19	.;.;T
Eigen	Benign	-0.25
Eigen_PC	Benign	-0.37
FATHMM_MKL	Benign	0.18	N
LIST_S2	Benign	0.71	T;T;T
M_CAP	Uncertain	0.20	D
MetaRNN	Benign	0.23	T;T;T
MetaSVM	Uncertain	0.20	D
MutationAssessor	Benign	1.5	.;.;L
PrimateAI	Benign	0.32	T
PROVEAN	Uncertain	-2.4	.;N;D
REVEL	Benign	0.22
Sift	Uncertain	0.0010	.;D;D
Sift4G	Uncertain	0.014	.;D;D
Vest4		0.28, 0.18
MutPred		0.34		.;.;Gain of methylation at P609 (P = 0.0351);
MVP		0.80
MPC		0.16
ClinPred		0.85	D
GERP RS		3.6
Varity_R		0.055
gMVP		0.13

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

Publications

No publications associated with this variant yet.

Other links and lift over

hg19: chr7-144094583;