9-99865020-A-C

Variant summary

Our verdict is Uncertain significance. Variant got 0 ACMG points: 2P and 2B. PM2BP4_Moderate

The NM_006981.4(NR4A3):​c.*1153A>C variant causes a 3 prime UTR 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: 31)

Consequence

NR4A3
NM_006981.4 3_prime_UTR

Scores

2

Clinical Significance

Not reported in ClinVar

Conservation

PhyloP100: 5.18
Variant links:
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]
STX17-DT (HGNC:51174): (STX17 divergent transcript)

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ACMG classification

Classification made for transcript

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 (BayesDel_noAF=-0.46).

Transcripts

RefSeq

Gene Transcript HGVSc HGVSp Effect #exon/exons MANE UniProt
NR4A3NM_006981.4 linkuse as main transcriptc.*1153A>C 3_prime_UTR_variant 8/8 ENST00000395097.7
NR4A3NM_173200.3 linkuse as main transcriptc.*1153A>C 3_prime_UTR_variant 9/9
NR4A3XM_017015162.2 linkuse as main transcriptc.*1153A>C 3_prime_UTR_variant 9/9

Ensembl

Gene Transcript HGVSc HGVSp Effect #exon/exons TSL MANE Appris UniProt
NR4A3ENST00000395097.7 linkuse as main transcriptc.*1153A>C 3_prime_UTR_variant 8/81 NM_006981.4 P1Q92570-1
STX17-DTENST00000655615.1 linkuse as main transcriptn.179-25945T>G intron_variant, non_coding_transcript_variant
NR4A3ENST00000330847.1 linkuse as main transcriptc.*1153A>C 3_prime_UTR_variant 7/75 Q92570-3
NR4A3ENST00000618101.4 linkuse as main transcriptc.*1153A>C 3_prime_UTR_variant 9/95 Q92570-3

Frequencies

GnomAD3 genomes
Cov.:
31
GnomAD4 exome
Cov.:
0
GnomAD4 genome
Cov.:
31

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name
Calibrated prediction
Score
Prediction
BayesDel_noAF
Benign
-0.46
CADD
Benign
11
DANN
Benign
0.84

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

LitVar

Below is the list of publications found by LitVar. It may be empty.

Other links and lift over

dbSNP: rs1131339; hg19: chr9-102627302; API