chr9-99828706-A-C

Variant names:

• chr9-99828706-A-C
• NM_006981.4:c.664A>C
• NR4A3 p.Ser222Arg

Variant summary

Our verdict is Uncertain significance. The variant received 1 ACMG points: 2P and 1B. PM2 BP4

The NM_006981.4(NR4A3):​c.664A>C​(p.Ser222Arg) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000258 in 1,160,868 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar. Another nucleotide change resulting in the same amino acid substitution has been previously reported as Uncertain significance in ClinVar. Another variant affecting the same amino acid position, but resulting in a different missense (i.e. S222N) has been classified as Uncertain significance.

• Frequency:
  • Genomes: not found (cov: 32)
  • Exomes 𝑓: 0.0000026 (0 hom.)
• Consequence: NR4A3 NM_006981.4 missense
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.475
• Publications: 0 publications found

Genes affected

NR4A3 (HGNC:7982): (nuclear receptor subfamily 4 group A member 3) This gene encodes a member of the steroid-thyroid hormone-retinoid receptor superfamily. The encoded protein may act as a transcriptional activator. The protein can efficiently bind the NGFI-B Response Element (NBRE). Three different versions of extraskeletal myxoid chondrosarcomas (EMCs) are the result of reciprocal translocations between this gene and other genes. The translocation breakpoints are associated with Nuclear Receptor Subfamily 4, Group A, Member 3 (on chromosome 9) and either Ewing Sarcome Breakpoint Region 1 (on chromosome 22), RNA Polymerase II, TATA Box-Binding Protein-Associated Factor, 68-KD (on chromosome 17), or Transcription factor 12 (on chromosome 15). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

NAMA (HGNC:42408): (non-protein coding RNA, associated with MAP kinase pathway and growth arrest)

ACMG classification

Our verdict: Uncertain_significance. The variant received 1 ACMG points.

• PM2: Very rare variant in population databases, with high coverage
• BP4: Computational evidence support a benign effect (MetaRNN=0.33446264).

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_006981.4. 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
	NR4A3	NM_006981.4	MANE Select	c.664A>C	p.Ser222Arg	missense	Exon 3 of 8	NP_008912.2
	NR4A3	NM_173200.3		c.697A>C	p.Ser233Arg	missense	Exon 4 of 9	NP_775292.1	Q92570-3
	NR4A3	NM_173199.4		c.664A>C	p.Ser222Arg	missense	Exon 3 of 5	NP_775291.1	Q92570-2

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	NR4A3	ENST00000395097.7	TSL:1 MANE Select	c.664A>C	p.Ser222Arg	missense	Exon 3 of 8	ENSP00000378531.2	Q92570-1
	NR4A3	ENST00000338488.8	TSL:1	c.664A>C	p.Ser222Arg	missense	Exon 3 of 5	ENSP00000340301.4	Q92570-2
	NR4A3	ENST00000330847.1	TSL:5	c.697A>C	p.Ser233Arg	missense	Exon 2 of 7	ENSP00000333122.1	Q92570-3

Frequencies

GnomAD3 genomes Cov.: 32

GnomAD4 exome AF: 0.00000258 AC: 3 AN: 1160868 Hom.: 0 Cov.: 31 AF XY: 0.00000178 AC XY: 1 AN XY: 562058

African (AFR) AF: 0.00 AC: 0 AN: 23188

American (AMR) AF: 0.00 AC: 0 AN: 8824

Ashkenazi Jewish (ASJ) AF: 0.00 AC: 0 AN: 15336

East Asian (EAS) AF: 0.00 AC: 0 AN: 26712

South Asian (SAS) AF: 0.00 AC: 0 AN: 41642

European-Finnish (FIN) AF: 0.00 AC: 0 AN: 26070

Middle Eastern (MID) AF: 0.00 AC: 0 AN: 3236

European-Non Finnish (NFE) AF: 0.00000310 AC: 3 AN: 968952

Other (OTH) AF: 0.00 AC: 0 AN: 46908

GnomAD4 genome Cov.: 32

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
AlphaMissense	Uncertain	0.50
BayesDel_addAF	Uncertain	0.060	T
BayesDel_noAF	Benign	-0.15
CADD	Benign	19
DANN	Benign	0.91
DEOGEN2	Benign	0.23	T
Eigen	Benign	-0.26
Eigen_PC	Benign	-0.13
FATHMM_MKL	Benign	0.64	D
LIST_S2	Benign	0.75	T
M_CAP	Pathogenic	0.89	D
MetaRNN	Benign	0.33	T
MetaSVM	Uncertain	-0.15	T
MutationAssessor	Benign	1.4	L
PhyloP100		0.47
PrimateAI	Pathogenic	0.91	D
PROVEAN	Benign	-0.46	N
REVEL	Uncertain	0.49
Sift	Benign	0.49	T
Sift4G	Benign	0.60	T
Varity_R		0.17
gMVP		0.48
Mutation Taster		=89/11	polymorphism

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

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr9-102590988;